From b413eee53fa3cc22a6bd4e03c9ac64bf26b7c834 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Wed, 26 Jan 2011 13:17:56 +0000 Subject: [PATCH] Replacing web site content with fresh version from JWS2 (JABAWS production ) branch git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@3640 e3abac25-378b-4346-85de-24260fe3988d --- website/Example_template.pdf | Bin 0 -> 56257 bytes website/develhome.html | 127 + website/dm_javadoc/allclasses-frame.html | 87 + website/dm_javadoc/allclasses-noframe.html | 87 + website/dm_javadoc/compbio/data/msa/MsaWS.html | 556 +++ .../compbio/data/msa/class-use/MsaWS.html | 189 + .../dm_javadoc/compbio/data/msa/package-frame.html | 32 + .../compbio/data/msa/package-summary.html | 176 + .../dm_javadoc/compbio/data/msa/package-tree.html | 151 + .../dm_javadoc/compbio/data/msa/package-use.html | 171 + .../compbio/data/sequence/Alignment.html | 403 ++ .../compbio/data/sequence/AlignmentMetadata.html | 329 ++ 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Services (JABAWS) developers documentation + + + + + + + +
+ + +
+ + +
+ +

JABAWS Javadoc

+

Data model javadoc- read this if your are coding against JABA Web Services

+

Complete javadoc - for developers who want to use JABAWS framework and use Engines and Executables directly

+

Starting up from the source code

+

SVN source repository:https://svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA_r1
+The repository contains a complete JABAWS Eclipse project. To use Eclipse with this repository you need to install Eclipse SVN plugin which could be found here: http://subclipse.tigris.org/servlets/ProjectProcess?pageID=p4wYuA. Eclipse update web site address is http://subclipse.tigris.org/update_1.4.x Take care to install 1.4.x version of the plugin, as SVN repository will not work with more recent clients. it would help to install TestNG plugin as well which could be downloaded from http://testng.org/doc/download.html. Please note however that no generated code is stored in the repository. That is to say that if you like to obtain client or server packages it is better to download them from the download section of this web site. Of cause If you want to make a modification to the source code you would need to generate distributives yourself. To do that first generate JAX-WS artifacts using build-server task from wsbuild.xml ant script, than you could use build.xml tasks to generate any of the distributives you need.

+

Structure of the project

+JABAWS layers +

Layers in the source code are defined in a different source folders which are: +
/webservices
+ /runner
+ /engine
+ /datamodel

+

JABAWS project is split into 4 layers. From bottom-up the first layer consists from the value classes used by all other layers of the hierarchy, in particular web services. So, to be able to use JABAWS one needs to have these classes. At the same time classes on this layer does not have any dependencies on the layers above.

+

The second layer contains code for execution of the wrappers, which are the abstraction describing native executables. The code on this level code engine. JABAWS can execute tasks locally that is on the same machine as JVM and on the cluster. Thus currently code on this layer contain two engines. This layer depends on the layer underneath, the data model layer, but is completely independent from the code above.

+

The third layer consists of the wrappers for the native executables and classes to handle their configuration. It depends on the engines and the data model, but know nothing about the web services.

+

Finally, the upper layer contains the web services, that depend on all the layers below.

+

The layer isolation is archived though specially designed compilation task which is executed sequentially in several stages so that the first layer compiles before any other layers, second layer compiles after that and process continies before all the code is compiled. Any violation of the layer boundaries results in the compilation failure. Use Ant "Compile" or "Complile_with_debug" tasks to perform the staged compilation.

+

A client package contains only classes from data model layer and a simple web services client. Framework package is for anyone who want to use JABAWS framework for controlling native executables in local or cluster environments. Framework exclude the web services layer. Server package contains all the code.

+ +

Running tests

+

The test results for the JABAWS package offered for download can be found here: Test Results
+JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse which has functionality similar to JUnit. However, no plugins are necessary to run the test cases, as testng jar is supplied with JABAWS together with an ant tasks to run the test cases.

+

The best way to ensure that JABAWS framework is completely functional on your system is to run all test cases. +Test cases tests all aspects of JABAWS functionality. Consequently, one need to have non windows operation system and support of the cluster to be able to run all tests. If your system does not support cluster, then you could run all test excluding those that depends on the cluster. +Several testing groups are supported: +

    +
  • All tests (Test)
    • +
  • Cluster tests (Run_cluster_dependent_test)
    • +
  • Cluster independent tests ()
    • +
  • Windows only tests (All_cluster_independent_windows_only_tests)
    • +
  • Performance and stability tests (Long_tests)
    • +
  • Re-run failed tests (Rerun_failed_tests)
    • +
  • Run custom test (CustomTest)
    • +
+

To run the tests you need to download all sources from repository. Once you have done that, enter into the command line mode, change directory to the project directory and type: + ant -f build.xml <test group name>

+

. Make sure you have Apache Ant + installed and path to ant executable is defined in your path environmental variable. + Replace test group name with the one of the names given in the list above to run required group of tests e.g for running cluster only tests + use the following + command: ant -f build.xml Run_cluster_dependent_test + If you work under Linux you could use a simple script from the root folder of repository called runtests.sh This script simply contains a collection of the test commands described above and paths to java home directory and an ant executable, which you can define once for your system and then reuse. +

+

+

A handy feature of TestNG is its ability to re-run failed tests. Failed test ant file is stored in test-output/testng-failed.xml. and is used in the ant task called Rerun_failed_tests. So re-running failed tests requires no more work than running any other test group and could be accomplished with the command: ant -f build.xml Rerun_failed_tests CustomTest runs the test defined in the project root directory file called temp-testng-customsuite.xml. This file is generated by TestNG plugin every time you run the test from Eclipse. Thus an easy way to run a test in a different environment is to run it from Eclipse first and then from ant using a custom test procedure.

+

For cluster execution make sure that the property LD_LIBRARY_PATH defined in build.xml points to cluster engine LD libraries directory in your local system.

+ +

Preparing distributive's

+

There are a number of ant tasks aimed for preparing distributives for download. + Currently a few types of JABAWS packages are offered +

    +
  1. Client only (contains classes required to access JABA Web Services)
    2. +
  2. Platform specific JABAWS (windows and other)
    3. +
  3. JABA Web Services without JAXWS libraries ( a the runtime dependency)
    4. +
  4. JABAWS without binaries
    5. +
  5. JABAWS without binaries and jax-ws
    6. +
  6. JABAWS framework
    7. +
+

+ Corresponding build task names are: +
    +
  1. min-jaba-client
    2. +
  2. jaba-windows, jaba-complete
    3. +
  3. jaba-without-jaxws
    4. +
  4. jaba-no-binaries
    5. +
  5. jaba-no-jaxws-no-binaries
    6. +
  6. full-jaba-client
    7. +
+ +

The easiest way to build all distributives is to call build-all ant task. There are more tasks defined in build.xml than described here. They are mostly self explanatory.

+

If you made any changes to the data model and would like to generate a complete JABAWS distro make sure you have rebuilt jaxws artifact as described below.

+

Building web services artifacts

+

Server side artifacts should be rebuild whenever the data model, meta model or MSA interface were changed. To do that run build-server task from wsbuild.xml ant build file. WSDL files will be generated in webservices/compbio/ws/server/resource directory. It is not necessary to edit them if any of the JABAWS clients are used. However, if you would like to generate portable artifacts using wsimport based on the generated WSDL files then, <soap:address location="REPLACE_WITH_ACTUAL_URL"/>

+ +

must be replaced with an actual server URL including the web services context path. For example:

+

http://www.compbio.ac.uk:8080/ws

+

JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible.

+
+ + +
+
+ + + + + + diff --git a/website/dm_javadoc/allclasses-frame.html b/website/dm_javadoc/allclasses-frame.html new file mode 100644 index 0000000..c45a41e --- /dev/null +++ b/website/dm_javadoc/allclasses-frame.html @@ -0,0 +1,87 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
+ + + + + +
Alignment +
+AlignmentMetadata +
+Argument +
+ChunkHolder +
+ClustalAlignmentUtil +
+FastaSequence +
+JobExecutionException +
+JobStatus +
+JobSubmissionException +
+Jws2Client +
+Limit +
+LimitExceededException +
+LimitsManager +
+MsaWS +
+Option +
+Parameter +
+Preset +
+PresetManager +
+Program +
+ResultNotAvailableException +
+RunnerConfig +
+SequenceUtil +
+Services +
+UnknownFileFormatException +
+UnsupportedRuntimeException +
+ValueConstrain +
+ValueConstrain.Type +
+WrongParameterException +
+WSTester +
+
+ + + diff --git a/website/dm_javadoc/allclasses-noframe.html b/website/dm_javadoc/allclasses-noframe.html new file mode 100644 index 0000000..1120a19 --- /dev/null +++ b/website/dm_javadoc/allclasses-noframe.html @@ -0,0 +1,87 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
+ + + + + +
Alignment +
+AlignmentMetadata +
+Argument +
+ChunkHolder +
+ClustalAlignmentUtil +
+FastaSequence +
+JobExecutionException +
+JobStatus +
+JobSubmissionException +
+Jws2Client +
+Limit +
+LimitExceededException +
+LimitsManager +
+MsaWS +
+Option +
+Parameter +
+Preset +
+PresetManager +
+Program +
+ResultNotAvailableException +
+RunnerConfig +
+SequenceUtil +
+Services +
+UnknownFileFormatException +
+UnsupportedRuntimeException +
+ValueConstrain +
+ValueConstrain.Type +
+WrongParameterException +
+WSTester +
+
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/MsaWS.html b/website/dm_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..122814d --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,556 @@ + + + + + + +MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.msa +
+Interface MsaWS<T>

+
+
Type Parameters:
T - executable type / web service type
+
+
+
public interface MsaWS<T>
+ + +

+Multiple Sequence Alignment (MSA) Web Services Interface +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Stringalign(List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ booleancancelJob(String jobId) + +
+          Stop running the job jobId but leave its output untouched
+ StringcustomAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Align a list of sequences with options.
+ JobStatusgetJobStatus(String jobId) + +
+          Return the status of the job.
+ Limit<T>getLimit(String presetName) + +
+          Get a Limit for a preset.
+ LimitsManager<T>getLimits() + +
+          List Limits supported by a web service.
+ PresetManager<T>getPresets() + +
+          Get presets supported by a web service
+ AlignmentgetResult(String jobId) + +
+          Return the result of the job.
+ RunnerConfig<T>getRunnerOptions() + +
+          Get options supported by a web service
+ StringpresetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+ ChunkHolderpullExecStatistics(String jobId, + long position) + +
+          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
+  +

+ + + + + + + + +
+Method Detail
+ +

+align

+
+String align(List<FastaSequence> sequences)
+             throws UnsupportedRuntimeException,
+                    LimitExceededException,
+                    JobSubmissionException
+
+
Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or when the average + length of the sequences are greater then defined in the default Limit, + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to make sure of this +
Returns:
jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
InvalidParameterException - thrown if input list of FASTA sequences is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
+
+
+
+ +

+customAlign

+
+String customAlign(List<FastaSequence> sequences,
+                   List<Option<T>> options)
+                   throws UnsupportedRuntimeException,
+                          LimitExceededException,
+                          JobSubmissionException,
+                          WrongParameterException
+
+
Align a list of sequences with options. +

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
options - A list of Options +
Returns:
jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or their average + length exceeds what is defined by the limit
See Also:
Default Limit is used to decide whether the calculation will be + permitted or denied
+
+
+
+ +

+presetAlign

+
+String presetAlign(List<FastaSequence> sequences,
+                   Preset<T> preset)
+                   throws UnsupportedRuntimeException,
+                          LimitExceededException,
+                          JobSubmissionException,
+                          WrongParameterException
+
+
Align a list of sequences with preset. + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

+

+
Parameters:
sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
preset - A list of Options +
Returns:
String - jobId - unique identifier for the job +
Throws: +
JobSubmissionException - is thrown when the job could not be submitted due to the + following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
InvalidParameterException - thrown if input list of FASTA sequence is null or empty +
UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and + Mafft service is called +
LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit
See Also:
Preset
+
+
+
+ +

+getResult

+
+Alignment getResult(String jobId)
+                    throws ResultNotAvailableException
+
+
Return the result of the job. This method waits for the job + jobId to complete before return. +

+

+
Parameters:
jobId - a unique job identifier +
Returns:
Alignment +
Throws: +
ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown due to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
InvalidParameterException - thrown if jobId is empty or is not recognised e.g. in invalid + format
+
+
+
+ +

+cancelJob

+
+boolean cancelJob(String jobId)
+
+
Stop running the job jobId but leave its output untouched +

+

+ +
Returns:
true if job was cancelled successfully, false otherwise +
Throws: +
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
+
+
+
+ +

+getJobStatus

+
+JobStatus getJobStatus(String jobId)
+
+
Return the status of the job. +

+

+
Parameters:
jobId - - unique job identifier +
Returns:
JobStatus - status of the job +
Throws: +
InvalidParameterException - is thrown if jobId is empty or cannot be recognised e.g. in + invalid format
See Also:
JobStatus
+
+
+
+ +

+pullExecStatistics

+
+ChunkHolder pullExecStatistics(String jobId,
+                               long position)
+
+
Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then + 1kb data is available from the position to the end of the file, then it + returns all the data available from the position to the end of the file. +

+

+
Parameters:
jobId - - unique job identifier
position - - next position within the file to read +
Returns:
ChunkHolder - which contains a chunk of data and a next position + within the file from which no data has been read +
Throws: +
InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format and also if the position value is negative
See Also:
ChunkHolder
+
+
+
+ +

+getRunnerOptions

+
+RunnerConfig<T> getRunnerOptions()
+
+
Get options supported by a web service +

+

+ +
Returns:
RunnerConfig the list of options and parameters supported by a + web service.
+
+
+
+ +

+getPresets

+
+PresetManager<T> getPresets()
+
+
Get presets supported by a web service +

+

+ +
Returns:
PresetManager the object contains information about presets + supported by a web service
+
+
+
+ +

+getLimit

+
+Limit<T> getLimit(String presetName)
+
+
Get a Limit for a preset. +

+

+
Parameters:
presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
Returns:
Limit
+
+
+
+ +

+getLimits

+
+LimitsManager<T> getLimits()
+
+
List Limits supported by a web service. +

+

+ +
Returns:
LimitManager
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html new file mode 100644 index 0000000..2fd76ec --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/class-use/MsaWS.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.data.msa.MsaWS + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Interface
compbio.data.msa.MsaWS

+
+ + + + + + + + + +
+Packages that use MsaWS
compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + +
+Uses of MsaWS in compbio.ws.client
+  +

+ + + + + + + + + +
Methods in compbio.ws.client that return MsaWS
+static + + + + +
+<T> MsaWS<T>
+		Jws2Client.connect(String host, + Services service) + +
+          Connects to a web service by the host and the service name
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-frame.html b/website/dm_javadoc/compbio/data/msa/package-frame.html new file mode 100644 index 0000000..6228fea --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-frame.html @@ -0,0 +1,32 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + +compbio.data.msa + + + + +
+Interfaces  + +
+MsaWS
+ + + + diff --git a/website/dm_javadoc/compbio/data/msa/package-summary.html b/website/dm_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..26b6877 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,176 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+Package compbio.data.msa +

+Web Service interfaces for JAva Bioinformatics Analysis Web Services. +

+See: +
+          Description +

+ + + + + + + + + +
+Interface Summary
MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
+  + +

+

+Package compbio.data.msa Description +

+ +

+Web Service interfaces for JAva Bioinformatics Analysis Web Services. +

+ +

+

+
Version:
+
1.0 April 2010
+
Author:
+
Peter Troshin
+
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-tree.html b/website/dm_javadoc/compbio/data/msa/package-tree.html new file mode 100644 index 0000000..70a3ef3 --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-tree.html @@ -0,0 +1,151 @@ + + + + + + +compbio.data.msa Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Hierarchy For Package compbio.data.msa +

+
+
+
Package Hierarchies:
All Packages
+
+

+Interface Hierarchy +

+
    +
  • compbio.data.msa.MsaWS<T>
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/msa/package-use.html b/website/dm_javadoc/compbio/data/msa/package-use.html new file mode 100644 index 0000000..43e7f7c --- /dev/null +++ b/website/dm_javadoc/compbio/data/msa/package-use.html @@ -0,0 +1,171 @@ + + + + + + +Uses of Package compbio.data.msa + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Package
compbio.data.msa

+
+ + + + + + + + + +
+Packages that use compbio.data.msa
compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
+  +

+ + + + + + + + +
+Classes in compbio.data.msa used by compbio.ws.client
MsaWS + +
+          Multiple Sequence Alignment (MSA) Web Services Interface
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..5f14d30 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,403 @@ + + + + + + +Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class Alignment

+
+java.lang.Object
+  extended by compbio.data.sequence.Alignment
+
+
+
+
@Immutable
+public final class Alignment
extends Object
+ + +

+Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. It does not guarantee neither the uniqueness of the names of + sequences nor it guarantees the uniqueness of the sequences. +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
See Also:
FastaSequence, +AlignmentMetadata
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+          Please note that this implementation does not take the order of sequences + into account!
+ AlignmentMetadatagetMetadata() + +
+           
+ List<FastaSequence>getSequences() + +
+           
+ intgetSize() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Alignment

+
+public Alignment(List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
+
+
+
Parameters:
sequences -
program -
gapchar -
+
+
+ +

+Alignment

+
+public Alignment(List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
+
+
+
Parameters:
sequences -
metadata -
+
+ + + + + + + + +
+Method Detail
+ +

+getSequences

+
+public List<FastaSequence> getSequences()
+
+
+ +
Returns:
list of FastaSequence records
+
+
+
+ +

+getSize

+
+public int getSize()
+
+
+ +
Returns:
a number of sequence in the alignment
+
+
+
+ +

+getMetadata

+
+public AlignmentMetadata getMetadata()
+
+
+ +
Returns:
AlignmentMetadata object
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
Please note that this implementation does not take the order of sequences + into account! +

+

+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..62c0b14 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,329 @@ + + + + + + +AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class AlignmentMetadata

+
+java.lang.Object
+  extended by compbio.data.sequence.AlignmentMetadata
+
+
+
+
@Immutable
+public class AlignmentMetadata
extends Object
+ + +

+Alignment metadata e.g. method/program being used to generate the alignment + and its parameters +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
AlignmentMetadata(Program program, + char gapchar) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ chargetGapchar() + +
+           
+ ProgramgetProgram() + +
+           
+ inthashCode() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+AlignmentMetadata

+
+public AlignmentMetadata(Program program,
+                         char gapchar)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getProgram

+
+public Program getProgram()
+
+
+
+
+
+
+ +

+getGapchar

+
+public char getGapchar()
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..3cbace7 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,387 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class ClustalAlignmentUtil

+
+java.lang.Object
+  extended by compbio.data.sequence.ClustalAlignmentUtil
+
+
+
+
public final class ClustalAlignmentUtil
extends Object
+ + +

+Tools to read and write clustal formated files +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
Petr Troshin based on jimp class
+
+
+ +

+ + + + + + + + + + + +
+Field Summary
+static chargapchar + +
+          Dash char to be used as gap char in the alignments
+  + + + + + + + + + + +
+Constructor Summary
ClustalAlignmentUtil() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static booleanisValidClustalFile(InputStream input) + +
+          Please note this method closes the input stream provided as a parameter
+static AlignmentreadClustalFile(File file) + +
+           
+static AlignmentreadClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+static voidwriteClustalAlignment(OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+gapchar

+
+public static final char gapchar
+
+
Dash char to be used as gap char in the alignments +

+

+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+ClustalAlignmentUtil

+
+public ClustalAlignmentUtil()
+
+
+ + + + + + + + +
+Method Detail
+ +

+readClustalFile

+
+public static Alignment readClustalFile(InputStream instream)
+                                 throws IOException,
+                                        UnknownFileFormatException
+
+
Read Clustal formatted alignment. Limitations: Does not read consensus + + Sequence names as well as the sequences are not guaranteed to be unique! +

+

+ +
Throws: +
{@link - IOException} +
{@link - UnknownFileFormatException} +
IOException +
UnknownFileFormatException
+
+
+
+ +

+isValidClustalFile

+
+public static boolean isValidClustalFile(InputStream input)
+
+
Please note this method closes the input stream provided as a parameter +

+

+
Parameters:
input - +
Returns:
true if the file is recognised as Clustal formatted alignment, + false otherwise
+
+
+
+ +

+writeClustalAlignment

+
+public static void writeClustalAlignment(OutputStream outStream,
+                                         Alignment alignment)
+                                  throws IOException
+
+
Write Clustal formatted alignment Limitations: does not record the + consensus. Potential bug - records 60 chars length alignment where + Clustal would have recorded 50 chars. +

+

+
Parameters:
outStream -
alignment - +
Throws: +
IOException
+
+
+
+ +

+readClustalFile

+
+public static Alignment readClustalFile(File file)
+                                 throws UnknownFileFormatException,
+                                        IOException
+
+
+ +
Throws: +
UnknownFileFormatException +
IOException
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..f7ead48 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,471 @@ + + + + + + +FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class FastaSequence

+
+java.lang.Object
+  extended by compbio.data.sequence.FastaSequence
+
+
+
+
@Immutable
+public class FastaSequence
extends Object
+ + +

+A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it stores e.g. it could be nucleotide, + protein or even gapped alignment sequence! The only guarantee it makes is + that the sequence does not contain white space characters e.g. spaces, new + lines etc +

+ +

+

+
Version:
+
1.0 September 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
FastaSequence(String id, + String sequence) + +
+          Upon construction the any whitespace characters are removed from the + sequence
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static intcountMatchesInSequence(String theString, + String theRegExp) + +
+           
+ booleanequals(Object obj) + +
+           
+ StringgetFormatedSequence(int width) + +
+          Format sequence per width letter in one string.
+ StringgetFormattedFasta() + +
+           
+ StringgetId() + +
+          Gets the value of id
+ intgetLength() + +
+           
+ StringgetOnelineFasta() + +
+           
+ StringgetSequence() + +
+          Gets the value of sequence
+ inthashCode() + +
+           
+ StringtoString() + +
+          Same as oneLineFasta
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+FastaSequence

+
+public FastaSequence(String id,
+                     String sequence)
+
+
Upon construction the any whitespace characters are removed from the + sequence +

+

+
Parameters:
id -
sequence -
+
+ + + + + + + + +
+Method Detail
+ +

+getId

+
+public String getId()
+
+
Gets the value of id +

+

+ +
Returns:
the value of id
+
+
+
+ +

+getSequence

+
+public String getSequence()
+
+
Gets the value of sequence +

+

+ +
Returns:
the value of sequence
+
+
+
+ +

+countMatchesInSequence

+
+public static int countMatchesInSequence(String theString,
+                                         String theRegExp)
+
+
+
+
+
+
+ +

+getFormattedFasta

+
+public String getFormattedFasta()
+
+
+
+
+
+
+ +

+getOnelineFasta

+
+public String getOnelineFasta()
+
+
+ +
Returns:
one line name, next line sequence, no matter what the sequence + length is
+
+
+
+ +

+getFormatedSequence

+
+public String getFormatedSequence(int width)
+
+
Format sequence per width letter in one string. Without spaces. +

+

+ +
Returns:
multiple line formated sequence, one line width letters length
+
+
+
+ +

+getLength

+
+public int getLength()
+
+
+ +
Returns:
sequence length
+
+
+
+ +

+toString

+
+public String toString()
+
+
Same as oneLineFasta +

+

+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/Program.html b/website/dm_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..909a998 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,388 @@ + + + + + + +Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Enum Program

+
+java.lang.Object
+  extended by java.lang.Enum<Program>
+      extended by compbio.data.sequence.Program
+
+
+
All Implemented Interfaces:
Serializable, Comparable<Program>
+
+
+
+
public enum Program
extends Enum<Program>
+ + +

+The list of programmes that can produce alignments +

+ +

+

+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + +
+Enum Constant Summary
CLUSTAL + +
+          ClustalW
MAFFT + +
+          Mafft
MUSCLE + +
+          Muscle
Probcons + +
+          Probcons
Tcoffee + +
+          Tcoffee
+  + + + + + + + + + + + + + + + +
+Method Summary
+static ProgramvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Program[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+CLUSTAL

+
+public static final Program CLUSTAL
+
+
ClustalW +

+

+
+
+
+ +

+MAFFT

+
+public static final Program MAFFT
+
+
Mafft +

+

+
+
+
+ +

+MUSCLE

+
+public static final Program MUSCLE
+
+
Muscle +

+

+
+
+
+ +

+Tcoffee

+
+public static final Program Tcoffee
+
+
Tcoffee +

+

+
+
+
+ +

+Probcons

+
+public static final Program Probcons
+
+
Probcons +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static Program[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (Program c : Program.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static Program valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..de2bd93 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,673 @@ + + + + + + +SequenceUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class SequenceUtil

+
+java.lang.Object
+  extended by compbio.data.sequence.SequenceUtil
+
+
+
+
public final class SequenceUtil
extends Object
+ + +

+Utility class for operations on sequences +

+ +

+

+
Version:
+
1.0
+
Author:
+
Petr Troshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Field Summary
+static PatternAA + +
+          Valid Amino acids
+static PatternAMBIGUOUS_AA + +
+          Same as AA pattern but with two additional letters - XU
+static PatternAMBIGUOUS_NUCLEOTIDE + +
+          Ambiguous nucleotide
+static PatternDIGIT + +
+          A digit
+static PatternNON_AA + +
+          inversion of AA pattern
+static PatternNON_NUCLEOTIDE + +
+          Non nucleotide
+static PatternNONWORD + +
+          Non word
+static PatternNUCLEOTIDE + +
+          Nucleotides a, t, g, c, u
+static PatternWHITE_SPACE + +
+          A whitespace character: [\t\n\x0B\f\r]
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static StringcleanSequence(String sequence) + +
+          Removes all whitespace chars in the sequence string
+static voidcloseSilently(Logger log, + Closeable stream) + +
+          Closes the Closable and logs the exception if any
+static StringdeepCleanSequence(String sequence) + +
+          Removes all special characters and digits as well as whitespace chars + from the sequence
+static booleanisAmbiguosProtein(String sequence) + +
+          Check whether the sequence confirms to amboguous protein sequence
+static booleanisNonAmbNucleotideSequence(String sequence) + +
+          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
+static booleanisNucleotideSequence(FastaSequence s) + +
+           
+static booleanisProteinSequence(String sequence) + +
+           
+static List<FastaSequence>readFasta(InputStream inStream) + +
+          Reads fasta sequences from inStream into the list of FastaSequence + objects
+static voidwriteFasta(OutputStream os, + List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidwriteFasta(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
+static voidwriteFastaKeepTheStream(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+WHITE_SPACE

+
+public static final Pattern WHITE_SPACE
+
+
A whitespace character: [\t\n\x0B\f\r] +

+

+
+
+
+ +

+DIGIT

+
+public static final Pattern DIGIT
+
+
A digit +

+

+
+
+
+ +

+NONWORD

+
+public static final Pattern NONWORD
+
+
Non word +

+

+
+
+
+ +

+AA

+
+public static final Pattern AA
+
+
Valid Amino acids +

+

+
+
+
+ +

+NON_AA

+
+public static final Pattern NON_AA
+
+
inversion of AA pattern +

+

+
+
+
+ +

+AMBIGUOUS_AA

+
+public static final Pattern AMBIGUOUS_AA
+
+
Same as AA pattern but with two additional letters - XU +

+

+
+
+
+ +

+NUCLEOTIDE

+
+public static final Pattern NUCLEOTIDE
+
+
Nucleotides a, t, g, c, u +

+

+
+
+
+ +

+AMBIGUOUS_NUCLEOTIDE

+
+public static final Pattern AMBIGUOUS_NUCLEOTIDE
+
+
Ambiguous nucleotide +

+

+
+
+
+ +

+NON_NUCLEOTIDE

+
+public static final Pattern NON_NUCLEOTIDE
+
+
Non nucleotide +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+isNucleotideSequence

+
+public static boolean isNucleotideSequence(FastaSequence s)
+
+
+ +
Returns:
true is the sequence contains only letters a,c, t, g, u
+
+
+
+ +

+isNonAmbNucleotideSequence

+
+public static boolean isNonAmbNucleotideSequence(String sequence)
+
+
Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +

+

+
+
+
+
+ +

+cleanSequence

+
+public static String cleanSequence(String sequence)
+
+
Removes all whitespace chars in the sequence string +

+

+
Parameters:
sequence - +
Returns:
cleaned up sequence
+
+
+
+ +

+deepCleanSequence

+
+public static String deepCleanSequence(String sequence)
+
+
Removes all special characters and digits as well as whitespace chars + from the sequence +

+

+
Parameters:
sequence - +
Returns:
cleaned up sequence
+
+
+
+ +

+isProteinSequence

+
+public static boolean isProteinSequence(String sequence)
+
+
+
Parameters:
sequence - +
Returns:
true is the sequence is a protein sequence, false overwise
+
+
+
+ +

+isAmbiguosProtein

+
+public static boolean isAmbiguosProtein(String sequence)
+
+
Check whether the sequence confirms to amboguous protein sequence +

+

+
Parameters:
sequence - +
Returns:
return true only if the sequence if ambiguous protein sequence + Return false otherwise. e.g. if the sequence is non-ambiguous + protein or DNA
+
+
+
+ +

+writeFasta

+
+public static void writeFasta(OutputStream outstream,
+                              List<FastaSequence> sequences,
+                              int width)
+                       throws IOException
+
+
Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +

+

+
Parameters:
outstream -
sequences -
width - - the maximum number of characters to write in one line +
Throws: +
IOException
+
+
+
+ +

+writeFastaKeepTheStream

+
+public static void writeFastaKeepTheStream(OutputStream outstream,
+                                           List<FastaSequence> sequences,
+                                           int width)
+                                    throws IOException
+
+
+ +
Throws: +
IOException
+
+
+
+ +

+readFasta

+
+public static List<FastaSequence> readFasta(InputStream inStream)
+                                     throws IOException
+
+
Reads fasta sequences from inStream into the list of FastaSequence + objects +

+

+
Parameters:
inStream - from +
Returns:
list of FastaSequence objects +
Throws: +
IOException
+
+
+
+ +

+writeFasta

+
+public static void writeFasta(OutputStream os,
+                              List<FastaSequence> sequences)
+                       throws IOException
+
+
Writes FastaSequence in the file, each sequence will take one line only +

+

+
Parameters:
os -
sequences - +
Throws: +
IOException
+
+
+
+ +

+closeSilently

+
+public static final void closeSilently(Logger log,
+                                       Closeable stream)
+
+
Closes the Closable and logs the exception if any +

+

+
Parameters:
log -
stream -
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..6163110 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,300 @@ + + + + + + +UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Class UnknownFileFormatException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.data.sequence.UnknownFileFormatException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class UnknownFileFormatException
extends Exception
+ + +

+

+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + +
+Constructor Summary
UnknownFileFormatException() + +
+           
UnknownFileFormatException(File file, + Throwable cause) + +
+           
UnknownFileFormatException(String message) + +
+           
UnknownFileFormatException(String message, + Throwable cause) + +
+           
UnknownFileFormatException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException()
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(File file,
+                                  Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(String message,
+                                  Throwable cause)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(String message)
+
+
+
+ +

+UnknownFileFormatException

+
+public UnknownFileFormatException(Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..cfddffa --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,236 @@ + + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.Alignment

+
+ + + + + + + + + + + + + +
+Packages that use Alignment
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Alignment in compbio.data.msa
+  +

+ + + + + + + + + +
Methods in compbio.data.msa that return Alignment
+ AlignmentMsaWS.getResult(String jobId) + +
+          Return the result of the job.
+  +

+ + + + + +
+Uses of Alignment in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Alignment
+static AlignmentClustalAlignmentUtil.readClustalFile(File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence with parameters of type Alignment
+static voidClustalAlignmentUtil.writeClustalAlignment(OutputStream outStream, + Alignment alignment) + +
+          Write Clustal formatted alignment Limitations: does not record the + consensus.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html new file mode 100644 index 0000000..48f1339 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html @@ -0,0 +1,196 @@ + + + + + + +Uses of Class compbio.data.sequence.AlignmentMetadata + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.AlignmentMetadata

+
+ + + + + + + + + +
+Packages that use AlignmentMetadata
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of AlignmentMetadata in compbio.data.sequence
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence that return AlignmentMetadata
+ AlignmentMetadataAlignment.getMetadata() + +
+           
+  +

+ + + + + + + + +
Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html new file mode 100644 index 0000000..3fa8980 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.ClustalAlignmentUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.ClustalAlignmentUtil

+
+No usage of compbio.data.sequence.ClustalAlignmentUtil +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..4b31821 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,362 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Class
compbio.data.sequence.FastaSequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use FastaSequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
+  +

+ + + + + +
+Uses of FastaSequence in compbio.data.msa
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.msa with type arguments of type FastaSequence
+ StringMsaWS.align(List<FastaSequence> sequences) + +
+          Align a list of sequences with default settings.
+ StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
+          Align a list of sequences with options.
+ StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
+          Align a list of sequences with preset.
+  +

+ + + + + +
+Uses of FastaSequence in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that return types with arguments of type FastaSequence
+ List<FastaSequence>Alignment.getSequences() + +
+           
+static List<FastaSequence>SequenceUtil.readFasta(InputStream inStream) + +
+          Reads fasta sequences from inStream into the list of FastaSequence + objects
+  +

+ + + + + + + + + +
Methods in compbio.data.sequence with parameters of type FastaSequence
+static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) + +
+           
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.data.sequence with type arguments of type FastaSequence
+static voidSequenceUtil.writeFasta(OutputStream os, + List<FastaSequence> sequences) + +
+          Writes FastaSequence in the file, each sequence will take one line only
+static voidSequenceUtil.writeFasta(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
+static voidSequenceUtil.writeFastaKeepTheStream(OutputStream outstream, + List<FastaSequence> sequences, + int width) + +
+           
+  +

+ + + + + + + + + + + +
Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
Alignment(List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
+           
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
+  +

+ + + + + +
+Uses of FastaSequence in compbio.metadata
+  +

+ + + + + + + + + + + + + + + + + +
Method parameters in compbio.metadata with type arguments of type FastaSequence
+static intLimit.getAvgSequenceLength(List<FastaSequence> data) + +
+          Calculates an average sequence length of the dataset
+ booleanLimit.isExceeded(List<FastaSequence> data) + +
+          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
+static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/Program.html b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html new file mode 100644 index 0000000..44b0b3e --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/Program.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Program + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Uses of Class
compbio.data.sequence.Program

+
+ + + + + + + + + +
+Packages that use Program
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of Program in compbio.data.sequence
+  +

+ + + + + + + + + + + + + + + + + +
Methods in compbio.data.sequence that return Program
+ ProgramAlignmentMetadata.getProgram() + +
+           
+static ProgramProgram.valueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static Program[]Program.values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  +

+ + + + + + + + + + + +
Constructors in compbio.data.sequence with parameters of type Program
Alignment(List<FastaSequence> sequences, + Program program, + char gapchar) + +
+           
AlignmentMetadata(Program program, + char gapchar) + +
+           
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..123654c --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Uses of Class
compbio.data.sequence.SequenceUtil

+
+No usage of compbio.data.sequence.SequenceUtil +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..01c17dc --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+
+

+Uses of Class
compbio.data.sequence.UnknownFileFormatException

+
+ + + + + + + + + +
+Packages that use UnknownFileFormatException
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
+  +

+ + + + + +
+Uses of UnknownFileFormatException in compbio.data.sequence
+  +

+ + + + + + + + + + + + + +
Methods in compbio.data.sequence that throw UnknownFileFormatException
+static AlignmentClustalAlignmentUtil.readClustalFile(File file) + +
+           
+static AlignmentClustalAlignmentUtil.readClustalFile(InputStream instream) + +
+          Read Clustal formatted alignment.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-frame.html b/website/dm_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..fe45def --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,62 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + +compbio.data.sequence + + + + +
+Classes  + +
+Alignment +
+AlignmentMetadata +
+ClustalAlignmentUtil +
+FastaSequence +
+SequenceUtil
+ + + + + + +
+Enums  + +
+Program
+ + + + + + +
+Exceptions  + +
+UnknownFileFormatException
+ + + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-summary.html b/website/dm_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..1609e36 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,224 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+

+Package compbio.data.sequence +

+A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. +

+See: +
+          Description +

+ + + + + + + + + + + + + + + + + + + + + + + + + +
+Class Summary
AlignmentMultiple sequence alignment.
AlignmentMetadataAlignment metadata e.g.
ClustalAlignmentUtilTools to read and write clustal formated files
FastaSequenceA FASTA formatted sequence.
SequenceUtilUtility class for operations on sequences
+  + +

+ + + + + + + + + +
+Enum Summary
ProgramThe list of programmes that can produce alignments
+  + +

+ + + + + + + + + +
+Exception Summary
UnknownFileFormatException 
+  + +

+

+Package compbio.data.sequence Description +

+ +

+A data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services. +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
Petr Troshin
+
+
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
+ PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-tree.html b/website/dm_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..e4ca7c3 --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,168 @@ + + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+
+

+Hierarchy For Package compbio.data.sequence +

+
+
+
Package Hierarchies:
All Packages
+
+

+Class Hierarchy +

+ +

+Enum Hierarchy +

+ +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
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+		 + +
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+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/data/sequence/package-use.html b/website/dm_javadoc/compbio/data/sequence/package-use.html new file mode 100644 index 0000000..11573ba --- /dev/null +++ b/website/dm_javadoc/compbio/data/sequence/package-use.html @@ -0,0 +1,240 @@ + + + + + + +Uses of Package compbio.data.sequence + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+
+

+Uses of Package
compbio.data.sequence

+
+ + + + + + + + + + + + + + + + + +
+Packages that use compbio.data.sequence
compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model. 
compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
+  +

+ + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.msa
Alignment + +
+          Multiple sequence alignment.
FastaSequence + +
+          A FASTA formatted sequence.
+  +

+ + + + + + + + + + + + + + + + + + + + +
+Classes in compbio.data.sequence used by compbio.data.sequence
Alignment + +
+          Multiple sequence alignment.
AlignmentMetadata + +
+          Alignment metadata e.g.
FastaSequence + +
+          A FASTA formatted sequence.
Program + +
+          The list of programmes that can produce alignments
UnknownFileFormatException + +
+           
+  +

+ + + + + + + + +
+Classes in compbio.data.sequence used by compbio.metadata
FastaSequence + +
+          A FASTA formatted sequence.
+  +

+

+ + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Argument.html b/website/dm_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..b500d00 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,327 @@ + + + + + + +Argument + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Interface Argument<T>

+
+
Type Parameters:
T - executable type
+
+
All Known Implementing Classes:
Option, Parameter
+
+
+
+
public interface Argument<T>
+ + +

+An unmodifiable view for the options and parameters, with one exception - it + allows to set a value +

+ +

+

+
Author:
+
pvtroshin + + Date December 2009
+
See Also:
Parameter, +Option
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ StringgetDefaultValue() + +
+           
+ StringgetDescription() + +
+           
+ URLgetFurtherDetails() + +
+           
+ StringgetName() + +
+           
+ List<String>getPossibleValues() + +
+           
+ voidsetValue(String defaultValue) + +
+          Set default values for the parameter or an option
+  +

+ + + + + + + + +
+Method Detail
+ +

+getFurtherDetails

+
+URL getFurtherDetails()
+
+
+
+
+
+
+ +

+getDefaultValue

+
+String getDefaultValue()
+
+
+
+
+
+
+ +

+getDescription

+
+String getDescription()
+
+
+
+
+
+
+ +

+getName

+
+String getName()
+
+
+
+
+
+
+ +

+getPossibleValues

+
+List<String> getPossibleValues()
+
+
+ +
Returns:
List of values allowed for an Argument
+
+
+
+ +

+setValue

+
+void setValue(String defaultValue)
+              throws WrongParameterException
+
+
Set default values for the parameter or an option +

+

+
Parameters:
defaultValue - the value to be set +
Throws: +
WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
See Also:
ValueConstrain
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..c898bcc --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,350 @@ + + + + + + +ChunkHolder + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class ChunkHolder

+
+java.lang.Object
+  extended by compbio.metadata.ChunkHolder
+
+
+
+
public class ChunkHolder
extends Object
+ + +

+Represents a chunk of a string data together with the position in a file for + the next read operation. +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
ChunkHolder(String chunk, + long position) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ StringgetChunk() + +
+           
+ longgetNextPosition() + +
+           
+ inthashCode() + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ChunkHolder

+
+public ChunkHolder(String chunk,
+                   long position)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getChunk

+
+public String getChunk()
+
+
+
+
+
+
+ +

+getNextPosition

+
+public long getNextPosition()
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..1e83666 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,279 @@ + + + + + + +JobExecutionException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class JobExecutionException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobExecutionException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class JobExecutionException
extends Exception
+ + +

+JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
JobExecutionException(String message) + +
+           
JobExecutionException(String message, + Throwable cause) + +
+           
JobExecutionException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobExecutionException

+
+public JobExecutionException(String message)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(Throwable cause)
+
+
+
+ +

+JobExecutionException

+
+public JobExecutionException(String message,
+                             Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobStatus.html b/website/dm_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..8728f80 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,465 @@ + + + + + + +JobStatus + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Enum JobStatus

+
+java.lang.Object
+  extended by java.lang.Enum<JobStatus>
+      extended by compbio.metadata.JobStatus
+
+
+
All Implemented Interfaces:
Serializable, Comparable<JobStatus>
+
+
+
+
public enum JobStatus
extends Enum<JobStatus>
+ + +

+The status of the job. +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Enum Constant Summary
CANCELLED + +
+          Jobs that has been cancelled
COLLECTED + +
+          Results has been collected
FAILED + +
+          Failed jobs
FINISHED + +
+          Finished jobs
PENDING + +
+          Jobs which are in the queue and awaiting execution reported for cluster + jobs only
RUNNING + +
+          Jobs that are running
STARTED + +
+          Job calculation has been started.
SUBMITTED + +
+          Job has been submitted.
UNDEFINED + +
+          Represents jobs with unknown status
+  + + + + + + + + + + + + + + + +
+Method Summary
+static JobStatusvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static JobStatus[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+PENDING

+
+public static final JobStatus PENDING
+
+
Jobs which are in the queue and awaiting execution reported for cluster + jobs only +

+

+
+
+
+ +

+RUNNING

+
+public static final JobStatus RUNNING
+
+
Jobs that are running +

+

+
+
+
+ +

+CANCELLED

+
+public static final JobStatus CANCELLED
+
+
Jobs that has been cancelled +

+

+
+
+
+ +

+FINISHED

+
+public static final JobStatus FINISHED
+
+
Finished jobs +

+

+
+
+
+ +

+FAILED

+
+public static final JobStatus FAILED
+
+
Failed jobs +

+

+
+
+
+ +

+UNDEFINED

+
+public static final JobStatus UNDEFINED
+
+
Represents jobs with unknown status +

+

+
+
+
+ +

+STARTED

+
+public static final JobStatus STARTED
+
+
Job calculation has been started. First status reported by the local + engine +

+

+
+
+
+ +

+SUBMITTED

+
+public static final JobStatus SUBMITTED
+
+
Job has been submitted. This status is only set for cluster jobs +

+

+
+
+
+ +

+COLLECTED

+
+public static final JobStatus COLLECTED
+
+
Results has been collected +

+

+
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static JobStatus[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (JobStatus c : JobStatus.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static JobStatus valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..59f457e --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,283 @@ + + + + + + +JobSubmissionException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class JobSubmissionException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
Direct Known Subclasses:
LimitExceededException, UnsupportedRuntimeException
+
+
+
+
public class JobSubmissionException
extends Exception
+ + +

+Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException. If + this exception is thrown the task has not been calculated +

+ +

+

+
Author:
+
pvtroshin + + Date December 2009
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
JobSubmissionException(String message) + +
+           
JobSubmissionException(String message, + Throwable cause) + +
+           
JobSubmissionException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+JobSubmissionException

+
+public JobSubmissionException(String message)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(Throwable cause)
+
+
+
+ +

+JobSubmissionException

+
+public JobSubmissionException(String message,
+                              Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Limit.html b/website/dm_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..51efd54 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,478 @@ + + + + + + +Limit + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Limit<T>

+
+java.lang.Object
+  extended by compbio.metadata.Limit<T>
+
+
+
Type Parameters:
T - the type of an executable for which this limit is defined.
+
+
+
public class Limit<T>
extends Object
+ + +

+A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. Also contains static method for determining the + number of sequence and their average length in the List +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
pvtroshin
+
See Also:
LimitsManager
+
+ +

+ + + + + + + + + + + + + + +
+Constructor Summary
Limit(int seqNumber, + int seqLength, + String preset) + +
+          Instantiate the limit
Limit(int seqNumber, + int seqLength, + String preset, + boolean isDefault) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ intgetAvgSeqLength() + +
+           
+static intgetAvgSequenceLength(List<FastaSequence> data) + +
+          Calculates an average sequence length of the dataset
+ StringgetPreset() + +
+           
+ intgetSeqNumber() + +
+           
+ inthashCode() + +
+           
+ booleanisDefault() + +
+           
+ booleanisExceeded(List<FastaSequence> data) + +
+          Checks if the number of sequences or their average length in the dataset + exceeds this limit.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             String preset)
+
+
Instantiate the limit +

+

+
Parameters:
seqNumber - the maximum number of sequences allowed for calculation. + Required
seqLength - the average length of the sequence, optional
preset - the name of preset if any, optional +
Throws: +
IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
+
+
+ +

+Limit

+
+public Limit(int seqNumber,
+             int seqLength,
+             String preset,
+             boolean isDefault)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPreset

+
+public String getPreset()
+
+
+
+
+
+
+ +

+getAvgSeqLength

+
+public int getAvgSeqLength()
+
+
+ +
Returns:
the allowed average sequence length
+
+
+
+ +

+getSeqNumber

+
+public int getSeqNumber()
+
+
+ +
Returns:
the maximum number of sequences allowed
+
+
+
+ +

+isDefault

+
+public boolean isDefault()
+
+
+ +
Returns:
true is this is a default limit to be used, false otherwise
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+isExceeded

+
+public boolean isExceeded(List<FastaSequence> data)
+
+
Checks if the number of sequences or their average length in the dataset + exceeds this limit. +

+

+
Parameters:
data - the dataset to measure +
Returns:
true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise. First check the number of sequences + in the dataset and if it exceeds the limit return true + irrespective of the average length. If the number of sequences in + the dataset is less than the limit and average length is defined, + then check whether the total number of letters (number of + sequence multiplied by the average sequence length) is greater + then the total number of letters in the dataset. Returns true if + the total number of letters in the dataset is greater than the + limit, false otherwise.
+
+
+
+ +

+getAvgSequenceLength

+
+public static int getAvgSequenceLength(List<FastaSequence> data)
+
+
Calculates an average sequence length of the dataset +

+

+
Parameters:
data - +
Returns:
an average sequence length in the input dataset
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/LimitExceededException.html b/website/dm_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..9fbf007 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,357 @@ + + + + + + +LimitExceededException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class LimitExceededException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.LimitExceededException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class LimitExceededException
extends JobSubmissionException
+ + +

+This exception is thrown if the task larger in size that the limit that + applies to the calculation. +

+ +

+

+
Version:
+
1.0 February 2010
+
Author:
+
pvtroshin
+
See Also:
Limit, +Serialized Form
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
LimitExceededException(String message) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ intgetActualNumberofSequences() + +
+           
+ intgetNumberOfSequencesAllowed() + +
+           
+ intgetSequenceLenghtActual() + +
+           
+ intgetSequenceLenghtAllowed() + +
+           
+static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitExceededException

+
+public LimitExceededException(String message)
+
+
+ + + + + + + + +
+Method Detail
+ +

+newLimitExceeded

+
+public static LimitExceededException newLimitExceeded(Limit<?> limit,
+                                                      List<FastaSequence> seqs)
+
+
+
+
+
+
+ +

+getNumberOfSequencesAllowed

+
+public int getNumberOfSequencesAllowed()
+
+
+
+
+
+
+ +

+getActualNumberofSequences

+
+public int getActualNumberofSequences()
+
+
+
+
+
+
+ +

+getSequenceLenghtAllowed

+
+public int getSequenceLenghtAllowed()
+
+
+
+
+
+
+ +

+getSequenceLenghtActual

+
+public int getSequenceLenghtActual()
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/LimitsManager.html b/website/dm_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..52a8aaf --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,363 @@ + + + + + + +LimitsManager + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class LimitsManager<T>

+
+java.lang.Object
+  extended by compbio.metadata.LimitsManager<T>
+
+
+
Type Parameters:
T - executable type
+
+
+
public class LimitsManager<T>
extends Object
+ + +

+A collection of Limits +

+ +

+

+
Version:
+
1.0 January 2010
+
Author:
+
pvtroshin
+
See Also:
Limit
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
LimitsManager() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Limit<T>getDefaultLimit() + +
+           
+ Limit<T>getLimitByName(String presetName) + +
+           
+ List<Limit<T>>getLimits() + +
+           
+ StringtoString() + +
+           
+ voidvalidate(PresetManager<T> presets) + +
+          Validate Limits
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+LimitsManager

+
+public LimitsManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getLimits

+
+public List<Limit<T>> getLimits()
+
+
+ +
Returns:
all limits defined for an executable T
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+getLimitByName

+
+public Limit<T> getLimitByName(String presetName)
+
+
+
Parameters:
presetName - +
Returns:
Limit defined for the executable T and presetName. If no limit is + defined for the presetName then default Limit is returned. If + presetName is empty or null than the default Limit will be + returned. If not limit defined for the type T than NULL will be + returned
+
+
+
+ +

+getDefaultLimit

+
+public Limit<T> getDefaultLimit()
+
+
+ +
Returns:
the default Limit for an executable type T
+
+
+
+ +

+validate

+
+public void validate(PresetManager<T> presets)
+              throws ValidationException
+
+
Validate Limits +

+

+
Parameters:
presets - +
Throws: +
ValidationException - if any of the Limit defined is found to be invalid. That is + when + + 1) No default limit is defined + + 2) More than 1 default limit is defined + + 3) Limit's preset name does not match any presets for type T
See Also:
Limit, +Preset
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Option.html b/website/dm_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..7fc0e28 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Option.html @@ -0,0 +1,822 @@ + + + + + + +Option + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Option<T>

+
+java.lang.Object
+  extended by compbio.metadata.Option<T>
+
+
+
Type Parameters:
T - type of executable
+
+
All Implemented Interfaces:
Argument<T>
+
+
+
Direct Known Subclasses:
Parameter
+
+
+
+
public class Option<T>
extends Object
implements Argument<T>
+ + +

+Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Field Summary
+protected  StringdefaultValue + +
+           
+protected  Stringdescription + +
+           
+protected  URLfurtherDetails + +
+           
+protected  booleanisRequired + +
+           
+protected  Stringname + +
+           
+  + + + + + + + + + + +
+Constructor Summary
Option(String name, + String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Set<String>addOptionNames(String... value) + +
+          Adds an option to the optionName list
+ booleanequals(Object obj) + +
+           
+ StringgetDefaultValue() + +
+          A default value of the option.
+ StringgetDescription() + +
+          A long description of the Option
+ URLgetFurtherDetails() + +
+          The URL where further details about the option can be found
+ StringgetName() + +
+          Human readable name of the option
+ List<String>getOptionNames() + +
+           
+ List<String>getPossibleValues() + +
+          List of possible optionNames
+ inthashCode() + +
+           
+ booleanisRequired() + +
+          Flag that indicated that this option must be specified in the command + line for an executable to run
+ voidsetDefaultValue(String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetDescription(String description) + +
+           
+ voidsetFurtherDetails(URL furtherDetails) + +
+           
+ voidsetName(String name) + +
+           
+ voidsetOptionNames(Set<String> optionNames) + +
+           
+ voidsetRequired(boolean isRequired) + +
+           
+ voidsetValue(String dValue) + +
+          Set default values for the parameter or an option
+ StringtoCommand(String nameValueSeparator) + +
+          Convert the option to the command string.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+description

+
+protected String description
+
+
+
+
+
+ +

+name

+
+protected String name
+
+
+
+
+
+ +

+isRequired

+
+protected boolean isRequired
+
+
+
+
+
+ +

+furtherDetails

+
+protected URL furtherDetails
+
+
+
+
+
+ +

+defaultValue

+
+protected String defaultValue
+
+
+
+
+ + + + + + + + +
+Constructor Detail
+ +

+Option

+
+public Option(String name,
+              String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getName

+
+public String getName()
+
+
Human readable name of the option +

+

+
Specified by:
getName in interface Argument<T>
+
+
+
+
+
+
+ +

+setName

+
+public void setName(String name)
+
+
+
+
+
+
+
+
+
+ +

+getDescription

+
+public String getDescription()
+
+
A long description of the Option +

+

+
Specified by:
getDescription in interface Argument<T>
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(String description)
+
+
+
+
+
+
+
+
+
+ +

+getFurtherDetails

+
+public URL getFurtherDetails()
+
+
The URL where further details about the option can be found +

+

+
Specified by:
getFurtherDetails in interface Argument<T>
+
+
+
+
+
+
+ +

+setFurtherDetails

+
+public void setFurtherDetails(URL furtherDetails)
+
+
+
+
+
+
+
+
+
+ +

+getDefaultValue

+
+public String getDefaultValue()
+
+
A default value of the option. Defaults to command line argument name + e.g. -auto +

+

+
Specified by:
getDefaultValue in interface Argument<T>
+
+
+
+
+
+
+ +

+setDefaultValue

+
+public void setDefaultValue(String defaultVal)
+                     throws WrongParameterException
+
+
Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

+

+
+
+
+
Parameters:
defaultVal - +
Throws: +
WrongParameterException - is thrown if the defaultValue is not found in optionList
+
+
+
+ +

+isRequired

+
+public boolean isRequired()
+
+
Flag that indicated that this option must be specified in the command + line for an executable to run +

+

+
+
+
+ +
Returns:
true is the option is required, false otherwise
+
+
+
+ +

+setRequired

+
+public void setRequired(boolean isRequired)
+
+
+
+
+
+
+
+
+
+ +

+getOptionNames

+
+public List<String> getOptionNames()
+
+
+
+
+
+ +
Returns:
List of option names
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(Set<String> optionNames)
+
+
+
+
+
+
+
+
+
+ +

+addOptionNames

+
+public Set<String> addOptionNames(String... value)
+
+
Adds an option to the optionName list +

+

+
+
+
+
Parameters:
value - +
Returns:
modified optionName list
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+toCommand

+
+public String toCommand(String nameValueSeparator)
+
+
Convert the option to the command string. +

+

+
+
+
+ +
Returns:
If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public List<String> getPossibleValues()
+
+
List of possible optionNames +

+

+
Specified by:
getPossibleValues in interface Argument<T>
+
+
+ +
Returns:
List of values allowed for an Argument
+
+
+
+ +

+setValue

+
+public void setValue(String dValue)
+              throws WrongParameterException
+
+
Description copied from interface: Argument
+
Set default values for the parameter or an option +

+

+
Specified by:
setValue in interface Argument<T>
+
+
+
Parameters:
dValue - the value to be set +
Throws: +
WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
See Also:
ValueConstrain
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Parameter.html b/website/dm_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..7a54dc1 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,590 @@ + + + + + + +Parameter + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Parameter<T>

+
+java.lang.Object
+  extended by compbio.metadata.Option<T>
+      extended by compbio.metadata.Parameter<T>
+
+
+
All Implemented Interfaces:
Argument<T>
+
+
+
+
public class Parameter<T>
extends Option<T>
+ + +

+A single value containing an option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues +

+ +

+

+
Version:
+
1.0 November 2009
+
Author:
+
pvtroshin
+
See Also:
Option, +Argument
+
+ +

+ + + + + + + +
+Field Summary
+  + + + + + + + +
Fields inherited from class compbio.metadata.Option
defaultValue, description, furtherDetails, isRequired, name
+  + + + + + + + + + + +
+Constructor Summary
Parameter(String name, + String description) + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Set<String>addOptionNames(String... value) + +
+          Adds an option to the optionName list
+ Set<String>addPossibleValues(String... value) + +
+           
+ booleanequals(Object obj) + +
+           
+ StringgetOptionName() + +
+           
+ List<String>getPossibleValues() + +
+          List is more convenient to work with
+ ValueConstraingetValidValue() + +
+           
+ inthashCode() + +
+           
+ voidsetDefaultValue(String defaultVal) + +
+          Sets one of the values defined in optionList as default.
+ voidsetOptionName(String optionName) + +
+           
+ voidsetOptionNames(Set<String> optionName) + +
+           
+ voidsetPossibleValues(Set<String> possibleValues) + +
+           
+ voidsetValidValue(ValueConstrain validValue) + +
+           
+ StringtoCommand(String nameValueSeparator) + +
+          Convert the option to the command string.
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class compbio.metadata.Option
getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Parameter

+
+public Parameter(String name,
+                 String description)
+
+
+ + + + + + + + +
+Method Detail
+ +

+getValidValue

+
+public ValueConstrain getValidValue()
+
+
+
+
+
+
+ +

+setValidValue

+
+public void setValidValue(ValueConstrain validValue)
+
+
+
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Option<T>
+
+
+
+
+
+
+ +

+toCommand

+
+public String toCommand(String nameValueSeparator)
+
+
Description copied from class: Option
+
Convert the option to the command string. +

+

+
Overrides:
toCommand in class Option<T>
+
+
+ +
Returns:
If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Option<T>
+
+
+
+
+
+
+ +

+getPossibleValues

+
+public List<String> getPossibleValues()
+
+
List is more convenient to work with +

+

+
Specified by:
getPossibleValues in interface Argument<T>
Overrides:
getPossibleValues in class Option<T>
+
+
+ +
Returns:
List of String
+
+
+
+ +

+setPossibleValues

+
+public void setPossibleValues(Set<String> possibleValues)
+
+
+
+
+
+
+ +

+addPossibleValues

+
+public Set<String> addPossibleValues(String... value)
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Option<T>
+
+
+
+
+
+
+ +

+setOptionNames

+
+public void setOptionNames(Set<String> optionName)
+
+
+
Overrides:
setOptionNames in class Option<T>
+
+
+
+
+
+
+ +

+addOptionNames

+
+public Set<String> addOptionNames(String... value)
+
+
Description copied from class: Option
+
Adds an option to the optionName list +

+

+
Overrides:
addOptionNames in class Option<T>
+
+
+ +
Returns:
modified optionName list
+
+
+
+ +

+getOptionName

+
+public String getOptionName()
+
+
+
+
+
+
+ +

+setOptionName

+
+public void setOptionName(String optionName)
+
+
+
+
+
+
+ +

+setDefaultValue

+
+public void setDefaultValue(String defaultVal)
+                     throws WrongParameterException
+
+
Description copied from class: Option
+
Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

+

+
Overrides:
setDefaultValue in class Option<T>
+
+
+ +
Throws: +
WrongParameterException - is thrown if the defaultValue is not found in optionList
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/Preset.html b/website/dm_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..e42c70d --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,455 @@ + + + + + + +Preset + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class Preset<T>

+
+java.lang.Object
+  extended by compbio.metadata.Preset<T>
+
+
+
Type Parameters:
T - executable type
+
+
+
public class Preset<T>
extends Object
+ + +

+Collection of Options and Parameters with their values +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
See Also:
Option, +Parameter
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
Preset() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ booleanequals(Object obj) + +
+           
+ List<Option<T>>getArguments(RunnerConfig<T> rconfig) + +
+          Converts list of options as String to type Option
+ StringgetDescription() + +
+           
+ StringgetName() + +
+           
+ List<String>getOptions() + +
+           
+ inthashCode() + +
+           
+ voidsetDescription(String description) + +
+           
+ voidsetName(String name) + +
+           
+ voidsetOptions(List<String> option) + +
+           
+ StringtoString() + +
+           
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+Preset

+
+public Preset()
+
+
+ + + + + + + + +
+Method Detail
+ +

+setOptions

+
+public void setOptions(List<String> option)
+
+
+
+
+
+
+ +

+setName

+
+public void setName(String name)
+
+
+
+
+
+
+ +

+setDescription

+
+public void setDescription(String description)
+
+
+
+
+
+
+ +

+getOptions

+
+public List<String> getOptions()
+
+
+ +
Returns:
a List of Options as a String
+
+
+
+ +

+getName

+
+public String getName()
+
+
+ +
Returns:
- name of the Preset
+
+
+
+ +

+getDescription

+
+public String getDescription()
+
+
+ +
Returns:
- a long description of the Preset
+
+
+
+ +

+getArguments

+
+public List<Option<T>> getArguments(RunnerConfig<T> rconfig)
+                             throws WrongParameterException
+
+
Converts list of options as String to type Option +

+

+
Parameters:
rconfig - +
Returns:
List of Options +
Throws: +
WrongParameterException - if the value of the parameter is invalid @see + Parameter
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/PresetManager.html b/website/dm_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..5ecd88a --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,428 @@ + + + + + + +PresetManager + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class PresetManager<T>

+
+java.lang.Object
+  extended by compbio.metadata.PresetManager<T>
+
+
+
Type Parameters:
T - type of executable.
+
+
+
public class PresetManager<T>
extends Object
+ + +

+Collection of presets and methods to manipulate them @see Preset +

+ +

+

+
Version:
+
1.0 December 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Field Summary
+static StringLOCAL_ENGINE_LIMIT_PRESET + +
+           
+  + + + + + + + + + + +
+Constructor Summary
PresetManager() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ Preset<T>getPresetByName(String presetName) + +
+           
+ List<Preset<T>>getPresets() + +
+           
+ StringgetRunnerClassName() + +
+           
+ voidsetPresets(List<Preset<T>> presets) + +
+           
+ voidsetRunnerClassName(String runnerClassName) + +
+           
+ StringtoString() + +
+           
+ voidvalidate(RunnerConfig<T> options) + +
+          Checks whether preset option and parameter are defined in RunnerConfig + object.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Field Detail
+ +

+LOCAL_ENGINE_LIMIT_PRESET

+
+public static final String LOCAL_ENGINE_LIMIT_PRESET
+
+
+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Constructor Detail
+ +

+PresetManager

+
+public PresetManager()
+
+
+ + + + + + + + +
+Method Detail
+ +

+getPresets

+
+public List<Preset<T>> getPresets()
+
+
+
+
+
+
+ +

+setPresets

+
+public void setPresets(List<Preset<T>> presets)
+
+
+
+
+
+
+ +

+getRunnerClassName

+
+public String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name of type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(String runnerClassName)
+
+
+
+
+
+
+ +

+getPresetByName

+
+public Preset<T> getPresetByName(String presetName)
+
+
+
Parameters:
presetName - +
Returns:
preset by its name, null if no preset found
+
+
+
+ +

+validate

+
+public void validate(RunnerConfig<T> options)
+              throws ValidationException
+
+
Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly! +

+

+ +
Throws: +
ValidationException - if preset is found to be invalid.
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..423c8b1 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,280 @@ + + + + + + +ResultNotAvailableException + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class ResultNotAvailableException

+
+java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.ResultNotAvailableException
+
+
+
All Implemented Interfaces:
Serializable
+
+
+
+
public class ResultNotAvailableException
extends Exception
+ + +

+ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides lower level exceptions + like DrmaaException +

+ +

+

+
Author:
+
pvtroshin + + Date October 2009
+
See Also:
Serialized Form
+
+ +

+ + + + + + + + + + + + + + + + + +
+Constructor Summary
ResultNotAvailableException(String message) + +
+           
ResultNotAvailableException(String message, + Throwable cause) + +
+           
ResultNotAvailableException(Throwable cause) + +
+           
+  + + + + + + + +
+Method Summary
+  + + + + + + + +
Methods inherited from class java.lang.Throwable
fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(String message)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(Throwable cause)
+
+
+
+ +

+ResultNotAvailableException

+
+public ResultNotAvailableException(String message,
+                                   Throwable cause)
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ + + diff --git a/website/dm_javadoc/compbio/metadata/RunnerConfig.html b/website/dm_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..0e8948a --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,706 @@ + + + + + + +RunnerConfig + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
+ + + +
+ +

+ +compbio.metadata +
+Class RunnerConfig<T>

+
+java.lang.Object
+  extended by compbio.metadata.RunnerConfig<T>
+
+
+
Type Parameters:
T - type of an Executable
+
+
+
@NotThreadSafe
+public class RunnerConfig<T>
extends Object
+ + +

+The list of Parameters and Options supported by executable. + The lists is defined in and loaded from Parameters.xml file. +

+ +

+

+
Version:
+
1.0 October 2009
+
Author:
+
pvtroshin
+
+
+ +

+ + + + + + + + + + + +
+Constructor Summary
RunnerConfig() + +
+           
+  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+ voidaddOption(Option<T> option) + +
+          Adds Option to the internal list of options
+ voidaddParameter(Parameter<T> param) + +
+          Adds parameter to the internal parameter list
+ RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
+           
+ booleanequals(Object obj) + +
+           
+ Option<T>getArgument(String name) + +
+          Returns the argument by its name if found, NULL otherwise.
+ Option<T>getArgumentByOptionName(String optionName) + +
+          Returns the argument by option name, NULL if the argument is not found
+ List<Option<T>>getArguments() + +
+          Returns list of Parameter and Option supported by current + runner
+ List<Option<T>>getOptions() + +
+          Returns the list of the Options supported by the executable of type T
+ List<Parameter<T>>getParameters() + +
+          Returns the list of parameters supported executable of type T.
+ StringgetPrmSeparator() + +
+           
+ StringgetRunnerClassName() + +
+           
+ booleanremoveArgument(String name) + +
+          Removes the argument Argument if found.
+ booleanremoveArgumentByOptionName(String optionName) + +
+          Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor.
+ voidsetOptions(List<Option<T>> parameters) + +
+          Adds the list of options or parameters to the internal list of options
+ voidsetParameters(List<Parameter<T>> parameters) + +
+          Sets the list of parameters as internal list
+ voidsetPrmSeparator(String prmSeparator) + +
+          Sets name value separator character
+ voidsetRunnerClassName(String runnerClassName) + +
+          Set the name of a runner class
+ StringtoString() + +
+           
+ voidvalidate() + +
+          Validate the value of the argument.
+  + + + + + + + +
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Constructor Detail
+ +

+RunnerConfig

+
+public RunnerConfig()
+
+
+ + + + + + + + +
+Method Detail
+ +

+copyAndValidateRConfig

+
+public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
+
+
+
+
+
+
+ +

+getOptions

+
+public List<Option<T>> getOptions()
+
+
Returns the list of the Options supported by the executable of type T +

+

+ +
Returns:
list of Option supported by type T
See Also:
Option
+
+
+
+ +

+addParameter

+
+public void addParameter(Parameter<T> param)
+
+
Adds parameter to the internal parameter list +

+

+
Parameters:
param - the Parameter to add
See Also:
Parameter
+
+
+
+ +

+addOption

+
+public void addOption(Option<T> option)
+
+
Adds Option to the internal list of options +

+

+
Parameters:
option - the Option to add
+
+
+
+ +

+getArguments

+
+public List<Option<T>> getArguments()
+
+
Returns list of Parameter and Option supported by current + runner +

+

+ +
Returns:
list of Option and Parameter supported by type T
+
+
+
+ +

+getPrmSeparator

+
+public String getPrmSeparator()
+
+
+ +
Returns:
name value separator character
+
+
+
+ +

+setPrmSeparator

+
+public void setPrmSeparator(String prmSeparator)
+
+
Sets name value separator character +

+

+
Parameters:
prmSeparator - the separator char
+
+
+
+ +

+setOptions

+
+public void setOptions(List<Option<T>> parameters)
+
+
Adds the list of options or parameters to the internal list of options +

+

+
Parameters:
parameters - the list of parameters to add
+
+
+
+ +

+getRunnerClassName

+
+public String getRunnerClassName()
+
+
+ +
Returns:
fully qualified class name for type T
+
+
+
+ +

+setRunnerClassName

+
+public void setRunnerClassName(String runnerClassName)
+
+
Set the name of a runner class +

+

+
Parameters:
runnerClassName - the name of the executable wrapping class
+
+
+
+ +

+setParameters

+
+public void setParameters(List<Parameter<T>> parameters)
+
+
Sets the list of parameters as internal list +

+

+
Parameters:
parameters - the list of parameters
+
+
+
+ +

+getParameters

+
+public List<Parameter<T>> getParameters()
+
+
Returns the list of parameters supported executable of type T. Where + Parameter is an Option with value. +

+

+ +
Returns:
List of Parameter supported by type T.
+
+
+
+ +

+toString

+
+public String toString()
+
+
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+equals

+
+public boolean equals(Object obj)
+
+
+
Overrides:
equals in class Object
+
+
+
+
+
+
+ +

+getArgument

+
+public Option<T> getArgument(String name)
+
+
Returns the argument by its name if found, NULL otherwise. Where the + Argument is a common interface for Option and Parameter + therefore this method can return either. If you need to retrieve the + Option by its optionNames use @link + getArgumentByOptionName(String) method. The + difference between option name and optionName is explained by the + following example: + + 
+ Sequence type
+         
+         --nuc - Assume the sequences are nucleotide.
+         --amino - Assume the sequences are amino acid. 
+         --amino
+         --nuc
+         --auto
+
+ + In the example, the "Sequence type" is a name whereas --amino, --nuc and + --auto are all optionNames. This dichotomy only manifests in + Option never in Parameters as the latter can + only have single element +

+

+
Parameters:
name - the Parameter of Option name +
Returns:
Argument
+
+
+
+ +

+removeArgument

+
+public boolean removeArgument(String name)
+
+
Removes the argument Argument if found. Where Argument is either + Option or Parameter. +

+

+
Parameters:
name - of the argument +
Returns:
true if argument was removed, false otherwise
+
+
+
+ +

+getArgumentByOptionName

+
+public Option<T> getArgumentByOptionName(String optionName)
+
+
Returns the argument by option name, NULL if the argument is not found +

+

+
Parameters:
optionName - - the optionName. This is not the same as an Option name. + + For example: + + 
+            Output sequences order
+                          --inputorder - Output order: same as input. 
+                           --reorder - Output order: aligned. Default: same as input
+                          --inputorder
+                          --reorder
+
+ + The name of the option in the example is + "Output sequences order" whereas optionNames are + "--inputorder" and "--reorder". If you need to retrieve the + Option or Parameter by its names use + getArgument(String) method +
Returns:
Option
+
+
+
+ +

+removeArgumentByOptionName

+
+public boolean removeArgumentByOptionName(String optionName)
+
+
Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor. +

+

+
Parameters:
optionName - the optionName of the option, do not confuse with the name! +
Returns:
true if argument with optionName exists and was removed, false + otherwise
See Also:
for destinctions + between optionNames and the name of the Option
+
+
+
+ +

+validate

+
+public void validate()
+              throws ValidationException
+
+
Validate the value of the argument. Checks whether the argument value is + in the valid values range. +

+

+ +
Throws: +
ValidationException - if any of the arguments found invalid which is when +
+
  • Parameter value outside ValueConstrain boundary
    • +
  • Parameter name is not listed in possible values
    • +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..dd5739b --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,265 @@ + + + + + + +UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class UnsupportedRuntimeException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.UnsupportedRuntimeException
+
    +
    +
    All Implemented Interfaces:
    Serializable
    +
    +
    +
    +
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    + + +

    +Indicates that the server could not execute native executables. e.g. If Mafft + (unix executable) is asked to be run on Windows. In context of JABAWS this + exception indicates that the service is deployed but is not able to run. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    UnsupportedRuntimeException(String message) + +
    +           
    UnsupportedRuntimeException(Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(String message)
    +
    +
    +
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..fbbe56c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,325 @@ + + + + + + +ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Enum ValueConstrain.Type

    +
    +java.lang.Object
+  extended by java.lang.Enum<ValueConstrain.Type>
+      extended by compbio.metadata.ValueConstrain.Type
+
    +
    +
    All Implemented Interfaces:
    Serializable, Comparable<ValueConstrain.Type>
    +
    +
    +
    Enclosing class:
    ValueConstrain
    +
    +
    +
    +
    public static enum ValueConstrain.Type
    extends Enum<ValueConstrain.Type>
    + + +

    +

    + +

    + + + + + + + + + + + + + +
    +Enum Constant Summary
    Float + +
    +           
    Integer + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ValueConstrain.TypevalueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +Integer

    +
    +public static final ValueConstrain.Type Integer
    +
    +
    +
    +
    +
    + +

    +Float

    +
    +public static final ValueConstrain.Type Float
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static ValueConstrain.Type[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (ValueConstrain.Type c : ValueConstrain.Type.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static ValueConstrain.Type valueOf(String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    IllegalArgumentException - if this enum type has no constant +with the specified name +
    NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/ValueConstrain.html b/website/dm_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..5968d9e --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,440 @@ + + + + + + +ValueConstrain + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class ValueConstrain

    +
    +java.lang.Object
+  extended by compbio.metadata.ValueConstrain
+
    +
    +
    +
    public class ValueConstrain
    extends Object
    + + +

    +The type and the lower and upper boundaries for numerical value. +

    + +

    +

    +
    Version:
    +
    1.0 November 2009
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classValueConstrain.Type + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ValueConstrain() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(Object obj) + +
    +           
    + NumbergetMax() + +
    +           
    + NumbergetMin() + +
    +           
    + ValueConstrain.TypegetType() + +
    +           
    + inthashCode() + +
    +           
    + voidsetMax(String max) + +
    +           
    + voidsetMin(String min) + +
    +           
    + voidsetType(ValueConstrain.Type type) + +
    +           
    + StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ValueConstrain

    +
    +public ValueConstrain()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getType

    +
    +public ValueConstrain.Type getType()
    +
    +
    +
    +
    +
    +
    + +

    +setType

    +
    +public void setType(ValueConstrain.Type type)
    +
    +
    +
    +
    +
    +
    + +

    +getMax

    +
    +public Number getMax()
    +
    +
    +
    +
    +
    +
    + +

    +setMax

    +
    +public void setMax(String max)
    +
    +
    +
    +
    +
    +
    + +

    +getMin

    +
    +public Number getMin()
    +
    +
    +
    +
    +
    +
    + +

    +setMin

    +
    +public void setMin(String min)
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(Object obj)
    +
    +
    +
    Overrides:
    equals in class Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public String toString()
    +
    +
    +
    Overrides:
    toString in class Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..f8703fe --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,294 @@ + + + + + + +WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class WrongParameterException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.WrongParameterException
+
    +
    +
    All Implemented Interfaces:
    Serializable
    +
    +
    +
    +
    public class WrongParameterException
    extends Exception
    + + +

    +WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value. +

    + +

    +

    +
    Version:
    +
    1.0 October 2009
    +
    Author:
    +
    pvtroshin
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterException(Option<?> option) + +
    +           
    WrongParameterException(String message) + +
    +           
    WrongParameterException(String message, + Throwable cause) + +
    +           
    WrongParameterException(Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Option<?> option)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(String message)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Throwable cause)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(String message,
+                               Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Argument.html b/website/dm_javadoc/compbio/metadata/class-use/Argument.html new file mode 100644 index 0000000..59618f6 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Argument.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.metadata.Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.metadata.Argument

    +
    + + + + + + + + + +
    +Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Argument in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Classes in compbio.metadata that implement Argument
    + classOption<T> + +
    +          Command line option/flag or multiple exclusive options with no value.
    + classParameter<T> + +
    +          A single value containing an option supported by the web service e.g.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html new file mode 100644 index 0000000..c36b0c5 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/ChunkHolder.html @@ -0,0 +1,182 @@ + + + + + + +Uses of Class compbio.metadata.ChunkHolder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ChunkHolder

    +
    + + + + + + + + + +
    +Packages that use ChunkHolder
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return ChunkHolder
    + ChunkHolderMsaWS.pullExecStatistics(String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html new file mode 100644 index 0000000..27480e2 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobExecutionException.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.metadata.JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobExecutionException

    +
    +No usage of compbio.metadata.JobExecutionException +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html new file mode 100644 index 0000000..e3d7c98 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobStatus.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Class compbio.metadata.JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobStatus

    +
    + + + + + + + + + + + + + +
    +Packages that use JobStatus
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return JobStatus
    + JobStatusMsaWS.getJobStatus(String jobId) + +
    +          Return the status of the job.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return JobStatus
    +static JobStatusJobStatus.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JobStatus[]JobStatus.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html new file mode 100644 index 0000000..1f7c42c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/JobSubmissionException.html @@ -0,0 +1,237 @@ + + + + + + +Uses of Class compbio.metadata.JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobSubmissionException

    +
    + + + + + + + + + + + + + +
    +Packages that use JobSubmissionException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw JobSubmissionException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Subclasses of JobSubmissionException in compbio.metadata
    + classLimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    + classUnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/class-use/Limit.html b/website/dm_javadoc/compbio/metadata/class-use/Limit.html new file mode 100644 index 0000000..aad5361 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/class-use/Limit.html @@ -0,0 +1,251 @@ + + + + + + +Uses of Class compbio.metadata.Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.Limit

    +
    + + + + + + + + + + + + + +
    +Packages that use Limit
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Limit
    + Limit<T>MsaWS.getLimit(String presetName) + +
    +          Get a Limit for a preset.
    +  +

    + + + + + +
    +Uses of Limit in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Limit
    + Limit<T>LimitsManager.getDefaultLimit() + +
    +           
    + Limit<T>LimitsManager.getLimitByName(String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Limit
    + List<Limit<T>>LimitsManager.getLimits() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +Packages that use LimitExceededException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw LimitExceededException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return LimitExceededException
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + List<FastaSequence> seqs) + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.LimitsManager

    +
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    +Packages that use LimitsManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return LimitsManager
    + LimitsManager<T>MsaWS.getLimits() + +
    +          List Limits supported by a web service.
    +  +

    +

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    +
    + + + + + + + + + + + + + +
    +Packages that use Option
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa
    +  +

    + + + + + + + + + +
    Method parameters in compbio.data.msa with type arguments of type Option
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    +  +

    + + + + + +
    +Uses of Option in compbio.metadata
    +  +

    + + + + + + + + + +
    Subclasses of Option in compbio.metadata
    + classParameter<T> + +
    +          A single value containing an option supported by the web service e.g.
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Option
    + Option<T>RunnerConfig.getArgument(String name) + +
    +          Returns the argument by its name if found, NULL otherwise.
    + Option<T>RunnerConfig.getArgumentByOptionName(String optionName) + +
    +          Returns the argument by option name, NULL if the argument is not found
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Option
    + List<Option<T>>RunnerConfig.getArguments() + +
    +          Returns list of Parameter and Option supported by current + runner
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + List<Option<T>>RunnerConfig.getOptions() + +
    +          Returns the list of the Options supported by the executable of type T
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Option
    + voidRunnerConfig.addOption(Option<T> option) + +
    +          Adds Option to the internal list of options
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Option
    + voidRunnerConfig.setOptions(List<Option<T>> parameters) + +
    +          Adds the list of options or parameters to the internal list of options
    +  +

    + + + + + + + + +
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) + +
    +           
    +  +

    +

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    +Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Parameter in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Parameter
    + List<Parameter<T>>RunnerConfig.getParameters() + +
    +          Returns the list of parameters supported executable of type T.
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Parameter
    + voidRunnerConfig.addParameter(Parameter<T> param) + +
    +          Adds parameter to the internal parameter list
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Parameter
    + voidRunnerConfig.setParameters(List<Parameter<T>> parameters) + +
    +          Sets the list of parameters as internal list
    +  +

    +

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    +Uses of Class
    compbio.metadata.Preset

    +
    + + + + + + + + + + + + + +
    +Packages that use Preset
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa with parameters of type Preset
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of Preset in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return Preset
    + Preset<T>PresetManager.getPresetByName(String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Preset
    + List<Preset<T>>PresetManager.getPresets() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Preset
    + voidPresetManager.setPresets(List<Preset<T>> presets) + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.PresetManager

    +
    + + + + + + + + + + + + + +
    +Packages that use PresetManager
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return PresetManager
    + PresetManager<T>MsaWS.getPresets() + +
    +          Get presets supported by a web service
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type PresetManager
    + voidLimitsManager.validate(PresetManager<T> presets) + +
    +          Validate Limits
    +  +

    +

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    +Uses of Class
    compbio.metadata.ResultNotAvailableException

    +
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    +Packages that use ResultNotAvailableException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that throw ResultNotAvailableException
    + AlignmentMsaWS.getResult(String jobId) + +
    +          Return the result of the job.
    +  +

    +

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    +Uses of Class
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    +
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    +Packages that use RunnerConfig
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return RunnerConfig
    + RunnerConfig<T>MsaWS.getRunnerOptions() + +
    +          Get options supported by a web service
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata with parameters of type RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidPresetManager.validate(RunnerConfig<T> options) + +
    +          Checks whether preset option and parameter are defined in RunnerConfig + object.
    +  +

    +

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    +Uses of Class
    compbio.metadata.UnsupportedRuntimeException

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    +Packages that use UnsupportedRuntimeException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    + StringMsaWS.align(List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.ValueConstrain.Type

    +
    + + + + + + + + + +
    +Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain.Type in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain.Type
    + ValueConstrain.TypeValueConstrain.getType() + +
    +           
    +static ValueConstrain.TypeValueConstrain.Type.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]ValueConstrain.Type.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    + voidValueConstrain.setType(ValueConstrain.Type type) + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.ValueConstrain

    +
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    +Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain
    + ValueConstrainParameter.getValidValue() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain
    + voidParameter.setValidValue(ValueConstrain validValue) + +
    +           
    +  +

    +

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    +
    +

    +Uses of Class
    compbio.metadata.WrongParameterException

    +
    + + + + + + + + + + + + + +
    +Packages that use WrongParameterException
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw WrongParameterException
    + StringMsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + StringMsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that throw WrongParameterException
    + List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidParameter.setDefaultValue(String defaultVal) + +
    +           
    + voidOption.setDefaultValue(String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidArgument.setValue(String defaultValue) + +
    +          Set default values for the parameter or an option
    + voidOption.setValue(String dValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-frame.html b/website/dm_javadoc/compbio/metadata/package-frame.html new file mode 100644 index 0000000..50c659c --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-frame.html @@ -0,0 +1,93 @@ + + + + + + +compbio.metadata + + + + + + + + + + + +compbio.metadata + + + + +
    +Interfaces  + +
    +Argument
    + + + + + + +
    +Classes  + +
    +ChunkHolder +
    +Limit +
    +LimitsManager +
    +Option +
    +Parameter +
    +Preset +
    +PresetManager +
    +RunnerConfig +
    +ValueConstrain
    + + + + + + +
    +Enums  + +
    +JobStatus +
    +ValueConstrain.Type
    + + + + + + +
    +Exceptions  + +
    +JobExecutionException +
    +JobSubmissionException +
    +LimitExceededException +
    +ResultNotAvailableException +
    +UnsupportedRuntimeException +
    +WrongParameterException
    + + + + diff --git a/website/dm_javadoc/compbio/metadata/package-summary.html b/website/dm_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..6256e43 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,286 @@ + + + + + + +compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.metadata +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. +

    +See: +
    +          Description +

    + + + + + + + + + +
    +Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    ChunkHolderRepresents a chunk of a string data together with the position in a file for + the next read operation.
    Limit<T>A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing an option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    +  + +

    + + + + + + + + + + + + + +
    +Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThis exception is thrown if the task larger in size that the limit that + applies to the calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  + +

    +

    +Package compbio.metadata Description +

    + +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of JAva Bioinformatics Analysis Web Services (JABAWS) +

    + +

    +

    +
    Version:
    +
    1.0 January 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-tree.html b/website/dm_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..6de85dc --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,178 @@ + + + + + + +compbio.metadata Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Hierarchy For Package compbio.metadata +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/metadata/package-use.html b/website/dm_javadoc/compbio/metadata/package-use.html new file mode 100644 index 0000000..3c74190 --- /dev/null +++ b/website/dm_javadoc/compbio/metadata/package-use.html @@ -0,0 +1,347 @@ + + + + + + +Uses of Package compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Package
    compbio.metadata

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.metadata
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder + +
    +          Represents a chunk of a string data together with the position in a file for + the next read operation.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.metadata
    Argument + +
    +          An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Parameter + +
    +          A single value containing an option supported by the web service e.g.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    ValueConstrain + +
    +          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type + +
    +           
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..85d990f --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,360 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class Jws2Client

    +
    +java.lang.Object
+  extended by compbio.ws.client.Jws2Client
+
    +
    +
    +
    public class Jws2Client
    extends Object
    + + +

    +A command line client for JAva Bioinformatics Analysis Web Services +

    + +

    +

    +
    Version:
    +
    1.0
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> MsaWS<T>
    +    		connect(String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +static StringgetHost(String[] cmd) + +
    +          Extracts host name from the command line
    +static StringgetServiceName(String[] cmd) + +
    +          Extracts service name from the command line
    +static voidmain(String[] args) + +
    +          Starts command line client, if no parameter are supported print help.
    +static booleanvalidURL(String urlstr) + +
    +          Attempt to construct the URL object from the string
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +validURL

    +
    +public static boolean validURL(String urlstr)
    +
    +
    Attempt to construct the URL object from the string +

    +

    +
    Parameters:
    urlstr - +
    Returns:
    true if it succeed false otherwise
    +
    +
    +
    + +

    +getServiceName

    +
    +public static String getServiceName(String[] cmd)
    +
    +
    Extracts service name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    service name or null if it is not defined
    +
    +
    +
    + +

    +getHost

    +
    +public static String getHost(String[] cmd)
    +
    +
    Extracts host name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    host name or null if it is not defined
    +
    +
    +
    + +

    +connect

    +
    +public static <T> MsaWS<T> connect(String host,
+                                   Services service)
+                        throws WebServiceException
    +
    +
    Connects to a web service by the host and the service name +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - +
    Returns:
    MsaWS +
    Throws: +
    WebServiceException
    +
    +
    +
    + +

    +main

    +
    +public static void main(String[] args)
    +
    +
    Starts command line client, if no parameter are supported print help. Two + parameters are required for successfull call the JWS2 host name and a + service name. +

    +

    +
    Parameters:
    args - Usage: -h=host_and_context + -s=serviceName ACTION [OPTIONS] + + -h= - a full URL to the JWS2 web server + including context path e.g. http://10.31.1.159:8080/ws + + -s= - one of [MafftWS, MuscleWS, ClustalWS, + TcoffeeWS, ProbconsWS] ACTIONS: + + -i= - full path to fasta formatted sequence file, + from which to align sequences + + -parameters - lists parameters supported by web service + + -presets - lists presets supported by web service + + -limits - lists web services limits Please note that if input + file is specified other actions are ignored + + OPTIONS: (only for use with -i action): + + -r= - name of the preset to use + + -o= - full path to the file where to write an + alignment -f= - the name of the file with + the list of parameters to use. Please note that -r and -f + options cannot be used together. Alignment is done with either + preset or a parameters from the file, but not both!
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/Services.html b/website/dm_javadoc/compbio/ws/client/Services.html new file mode 100644 index 0000000..c485461 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Services.html @@ -0,0 +1,412 @@ + + + + + + +Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Enum Services

    +
    +java.lang.Object
+  extended by java.lang.Enum<Services>
+      extended by compbio.ws.client.Services
+
    +
    +
    All Implemented Interfaces:
    Serializable, Comparable<Services>
    +
    +
    +
    +
    public enum Services
    extends Enum<Services>
    + + +

    +List of web services currently supported by JABAWS version 1 +

    + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    ClustalWS + +
    +           
    MafftWS + +
    +           
    MuscleWS + +
    +           
    ProbconsWS + +
    +           
    TcoffeeWS + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static ServicesgetService(Class wsImplClass) + +
    +           
    +static ServicesgetService(String servName) + +
    +           
    +static ServicesvalueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Services[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +MafftWS

    +
    +public static final Services MafftWS
    +
    +
    +
    +
    +
    + +

    +MuscleWS

    +
    +public static final Services MuscleWS
    +
    +
    +
    +
    +
    + +

    +ClustalWS

    +
    +public static final Services ClustalWS
    +
    +
    +
    +
    +
    + +

    +TcoffeeWS

    +
    +public static final Services TcoffeeWS
    +
    +
    +
    +
    +
    + +

    +ProbconsWS

    +
    +public static final Services ProbconsWS
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Services[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (Services c : Services.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static Services valueOf(String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    IllegalArgumentException - if this enum type has no constant +with the specified name +
    NullPointerException - if the argument is null
    +
    +
    +
    + +

    +getService

    +
    +public static Services getService(String servName)
    +
    +
    +
    +
    +
    +
    + +

    +getService

    +
    +public static Services getService(Class wsImplClass)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/dm_javadoc/compbio/ws/client/WSTester.html b/website/dm_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..ce5d917 --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,278 @@ + + + + + + +WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class WSTester

    +
    +java.lang.Object
+  extended by compbio.ws.client.WSTester
+
    +
    +
    +
    public class WSTester
    extends Object
    + + +

    +Class for testing web services +

    + +

    +

    +
    Version:
    +
    1.0 February 2010
    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSTester() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> void
    +    		main(String[] args) + +
    +          Test JWS2 web services
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WSTester

    +
    +public WSTester()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static <T> void main(String[] args)
+                 throws IOException
    +
    +
    Test JWS2 web services +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= + + -s= which is optional. If service name is not + provided then all known JWS2 web services are tested +
    Throws: +
    IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
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    +
    + + + + + + + + + +
    +Packages that use Services
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + +
    +Uses of Services in compbio.ws.client
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.client that return Services
    +static ServicesServices.getService(Class wsImplClass) + +
    +           
    +static ServicesServices.getService(String servName) + +
    +           
    +static ServicesServices.valueOf(String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Services[]Services.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client with parameters of type Services
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(String host, + Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

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    +Package compbio.ws.client +

    +A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + +
    +Class Summary
    Jws2ClientA command line client for JAva Bioinformatics Analysis Web Services
    WSTesterClass for testing web services
    +  + +

    + + + + + + + + + +
    +Enum Summary
    ServicesList of web services currently supported by JABAWS version 1
    +  + +

    +

    +Package compbio.ws.client Description +

    + +

    +A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. +

    + +

    +

    +
    Version:
    +
    1.0 April 2010
    +
    Author:
    +
    Peter Troshin
    +
    +
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    +Packages that use compbio.ws.client
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services. 
    +  +

    + + + + + + + + +
    +Classes in compbio.ws.client used by compbio.ws.client
    Services + +
    +          List of web services currently supported by JABAWS version 1
    +  +

    +

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    +compbio.data.*
    + +

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    compbio.data.sequence.ClustalAlignmentUtil
    +public static final chargapchar45
    + +

    + +

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    + +

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    compbio.metadata.PresetManager<T>
    +public static final StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
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    +

    +A

    +
    +
    AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Valid Amino acids +
    addOption(Option<T>) - +Method in class compbio.metadata.RunnerConfig +
    Adds Option to the internal list of options +
    addOptionNames(String...) - +Method in class compbio.metadata.Option +
    Adds an option to the optionName list +
    addOptionNames(String...) - +Method in class compbio.metadata.Parameter +
      +
    addParameter(Parameter<T>) - +Method in class compbio.metadata.RunnerConfig +
    Adds parameter to the internal parameter list +
    addPossibleValues(String...) - +Method in class compbio.metadata.Parameter +
      +
    align(List<FastaSequence>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with default settings. +
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - +Constructor for class compbio.data.sequence.Alignment +
      +
    Alignment(List<FastaSequence>, AlignmentMetadata) - +Constructor for class compbio.data.sequence.Alignment +
      +
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - +Constructor for class compbio.data.sequence.AlignmentMetadata +
      +
    AMBIGUOUS_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Same as AA pattern but with two additional letters - XU +
    AMBIGUOUS_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Ambiguous nucleotide +
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +
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    +L

    +
    +
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    Limit(int, int, String) - +Constructor for class compbio.metadata.Limit +
    Instantiate the limit +
    Limit(int, int, String, boolean) - +Constructor for class compbio.metadata.Limit +
      +
    LimitExceededException - Exception in compbio.metadata
    This exception is thrown if the task larger in size that the limit that + applies to the calculation.
    LimitExceededException(String) - +Constructor for exception compbio.metadata.LimitExceededException +
      +
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - +Constructor for class compbio.metadata.LimitsManager +
      +
    LOCAL_ENGINE_LIMIT_PRESET - +Static variable in class compbio.metadata.PresetManager +
      +
    +
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    +M

    +
    +
    main(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Starts command line client, if no parameter are supported print help. +
    main(String[]) - +Static method in class compbio.ws.client.WSTester +
    Test JWS2 web services +
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    +
    + + + + + + + + + + + + + + + +
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    +N

    +
    +
    name - +Variable in class compbio.metadata.Option +
      +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - +Static method in exception compbio.metadata.LimitExceededException +
      +
    NON_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    inversion of AA pattern +
    NON_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non nucleotide +
    NONWORD - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non word +
    NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Nucleotides a, t, g, c, u +
    +
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    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - +Constructor for class compbio.metadata.Option +
      +
    +
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    Parameter<T> - Class in compbio.metadata
    A single value containing an option supported by the web service e.g.
    Parameter(String, String) - +Constructor for class compbio.metadata.Parameter +
      +
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - +Constructor for class compbio.metadata.Preset +
      +
    presetAlign(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with preset. +
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - +Constructor for class compbio.metadata.PresetManager +
      +
    Program - Enum in compbio.data.sequence
    The list of programmes that can produce alignments
    pullExecStatistics(String, long) - +Method in interface compbio.data.msa.MsaWS +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. +
    +
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    readClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Read Clustal formatted alignment. +
    readClustalFile(File) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    readFasta(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +
    removeArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument Argument if found. +
    removeArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument which can be a Parameter or an Option instance by + the value in element of the runner configuration + descriptor. +
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    ResultNotAvailableException(String) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(String, Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - +Constructor for class compbio.metadata.RunnerConfig +
      +
    +
    + + + + + + + + + + + + + + + +
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    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    Services - Enum in compbio.ws.client
    List of web services currently supported by JABAWS version 1
    setDefaultValue(String) - +Method in class compbio.metadata.Option +
    Sets one of the values defined in optionList as default. +
    setDefaultValue(String) - +Method in class compbio.metadata.Parameter +
      +
    setDescription(String) - +Method in class compbio.metadata.Option +
      +
    setDescription(String) - +Method in class compbio.metadata.Preset +
      +
    setFurtherDetails(URL) - +Method in class compbio.metadata.Option +
      +
    setMax(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setMin(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setName(String) - +Method in class compbio.metadata.Option +
      +
    setName(String) - +Method in class compbio.metadata.Preset +
      +
    setOptionName(String) - +Method in class compbio.metadata.Parameter +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Option +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setOptions(List<String>) - +Method in class compbio.metadata.Preset +
      +
    setOptions(List<Option<T>>) - +Method in class compbio.metadata.RunnerConfig +
    Adds the list of options or parameters to the internal list of options +
    setParameters(List<Parameter<T>>) - +Method in class compbio.metadata.RunnerConfig +
    Sets the list of parameters as internal list +
    setPossibleValues(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setPresets(List<Preset<T>>) - +Method in class compbio.metadata.PresetManager +
      +
    setPrmSeparator(String) - +Method in class compbio.metadata.RunnerConfig +
    Sets name value separator character +
    setRequired(boolean) - +Method in class compbio.metadata.Option +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.PresetManager +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.RunnerConfig +
    Set the name of a runner class +
    setType(ValueConstrain.Type) - +Method in class compbio.metadata.ValueConstrain +
      +
    setValidValue(ValueConstrain) - +Method in class compbio.metadata.Parameter +
      +
    setValue(String) - +Method in interface compbio.metadata.Argument +
    Set default values for the parameter or an option +
    setValue(String) - +Method in class compbio.metadata.Option +
      +
    +
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    toCommand(String) - +Method in class compbio.metadata.Option +
    Convert the option to the command string. +
    toCommand(String) - +Method in class compbio.metadata.Parameter +
      +
    toString() - +Method in class compbio.data.sequence.Alignment +
      +
    toString() - +Method in class compbio.data.sequence.FastaSequence +
    Same as oneLineFasta +
    toString() - +Method in class compbio.metadata.ChunkHolder +
      +
    toString() - +Method in class compbio.metadata.Limit +
      +
    toString() - +Method in class compbio.metadata.LimitsManager +
      +
    toString() - +Method in class compbio.metadata.Option +
      +
    toString() - +Method in class compbio.metadata.Parameter +
      +
    toString() - +Method in class compbio.metadata.Preset +
      +
    toString() - +Method in class compbio.metadata.PresetManager +
      +
    toString() - +Method in class compbio.metadata.RunnerConfig +
      +
    toString() - +Method in class compbio.metadata.ValueConstrain +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(File, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    UnsupportedRuntimeException(Throwable) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    +
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    +
    validate(PresetManager<T>) - +Method in class compbio.metadata.LimitsManager +
    Validate Limits +
    validate(RunnerConfig<T>) - +Method in class compbio.metadata.PresetManager +
    Checks whether preset option and parameter are defined in RunnerConfig + object. +
    validate() - +Method in class compbio.metadata.RunnerConfig +
    Validate the value of the argument. +
    validURL(String) - +Static method in class compbio.ws.client.Jws2Client +
    Attempt to construct the URL object from the string +
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - +Constructor for class compbio.metadata.ValueConstrain +
      +
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - +Static method in enum compbio.data.sequence.Program +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.JobStatus +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.ws.client.Services +
    Returns the enum constant of this type with the specified name. +
    values() - +Static method in enum compbio.data.sequence.Program +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.JobStatus +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.ws.client.Services +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    cancelJob(String) - +Method in interface compbio.data.msa.MsaWS +
    Stop running the job jobId but leave its output untouched +
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of a string data together with the position in a file for + the next read operation.
    ChunkHolder(String, long) - +Constructor for class compbio.metadata.ChunkHolder +
      +
    cleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all whitespace chars in the sequence string +
    closeSilently(Logger, Closeable) - +Static method in class compbio.data.sequence.SequenceUtil +
    Closes the Closable and logs the exception if any +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - +Constructor for class compbio.data.sequence.ClustalAlignmentUtil +
      +
    compbio.data.msa - package compbio.data.msa
    Web Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.ws.client - package compbio.ws.client
    A command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    connect(String, Services) - +Static method in class compbio.ws.client.Jws2Client +
    Connects to a web service by the host and the service name +
    copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +
      +
    countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +
      +
    customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with options. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    WHITE_SPACE - +Static variable in class compbio.data.sequence.SequenceUtil +
    A whitespace character: [\t\n\x0B\f\r] +
    writeClustalAlignment(OutputStream, Alignment) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Write Clustal formatted alignment Limitations: does not record the + consensus. +
    writeFasta(OutputStream, List<FastaSequence>, int) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +
    writeFasta(OutputStream, List<FastaSequence>) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes FastaSequence in the file, each sequence will take one line only +
    writeFastaKeepTheStream(OutputStream, List<FastaSequence>, int) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    WrongParameterException(Option<?>) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String, Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - +Constructor for class compbio.ws.client.WSTester +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    deepCleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all special characters and digits as well as whitespace chars + from the sequence +
    defaultValue - +Variable in class compbio.metadata.Option +
      +
    description - +Variable in class compbio.metadata.Option +
      +
    DIGIT - +Static variable in class compbio.data.sequence.SequenceUtil +
    A digit +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    equals(Object) - +Method in class compbio.data.sequence.Alignment +
    Please note that this implementation does not take the order of sequences + into account! +
    equals(Object) - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    equals(Object) - +Method in class compbio.data.sequence.FastaSequence +
      +
    equals(Object) - +Method in class compbio.metadata.ChunkHolder +
      +
    equals(Object) - +Method in class compbio.metadata.Limit +
      +
    equals(Object) - +Method in class compbio.metadata.Option +
      +
    equals(Object) - +Method in class compbio.metadata.Parameter +
      +
    equals(Object) - +Method in class compbio.metadata.Preset +
      +
    equals(Object) - +Method in class compbio.metadata.RunnerConfig +
      +
    equals(Object) - +Method in class compbio.metadata.ValueConstrain +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - +Constructor for class compbio.data.sequence.FastaSequence +
    Upon construction the any whitespace characters are removed from the + sequence +
    furtherDetails - +Variable in class compbio.metadata.Option +
      +
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    +
    gapchar - +Static variable in class compbio.data.sequence.ClustalAlignmentUtil +
    Dash char to be used as gap char in the alignments +
    getActualNumberofSequences() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by its name if found, NULL otherwise. +
    getArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by option name, NULL if the argument is not found +
    getArguments(RunnerConfig<T>) - +Method in class compbio.metadata.Preset +
    Converts list of options as String to type Option +
    getArguments() - +Method in class compbio.metadata.RunnerConfig +
    Returns list of Parameter and Option supported by current + runner +
    getAvgSeqLength() - +Method in class compbio.metadata.Limit +
      +
    getAvgSequenceLength(List<FastaSequence>) - +Static method in class compbio.metadata.Limit +
    Calculates an average sequence length of the dataset +
    getChunk() - +Method in class compbio.metadata.ChunkHolder +
      +
    getDefaultLimit() - +Method in class compbio.metadata.LimitsManager +
      +
    getDefaultValue() - +Method in interface compbio.metadata.Argument +
      +
    getDefaultValue() - +Method in class compbio.metadata.Option +
    A default value of the option. +
    getDescription() - +Method in interface compbio.metadata.Argument +
      +
    getDescription() - +Method in class compbio.metadata.Option +
    A long description of the Option +
    getDescription() - +Method in class compbio.metadata.Preset +
      +
    getFormatedSequence(int) - +Method in class compbio.data.sequence.FastaSequence +
    Format sequence per width letter in one string. +
    getFormattedFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getFurtherDetails() - +Method in interface compbio.metadata.Argument +
      +
    getFurtherDetails() - +Method in class compbio.metadata.Option +
    The URL where further details about the option can be found +
    getGapchar() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getHost(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts host name from the command line +
    getId() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of id +
    getJobStatus(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the status of the job. +
    getLength() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getLimit(String) - +Method in interface compbio.data.msa.MsaWS +
    Get a Limit for a preset. +
    getLimitByName(String) - +Method in class compbio.metadata.LimitsManager +
      +
    getLimits() - +Method in interface compbio.data.msa.MsaWS +
    List Limits supported by a web service. +
    getLimits() - +Method in class compbio.metadata.LimitsManager +
      +
    getMax() - +Method in class compbio.metadata.ValueConstrain +
      +
    getMetadata() - +Method in class compbio.data.sequence.Alignment +
      +
    getMin() - +Method in class compbio.metadata.ValueConstrain +
      +
    getName() - +Method in interface compbio.metadata.Argument +
      +
    getName() - +Method in class compbio.metadata.Option +
    Human readable name of the option +
    getName() - +Method in class compbio.metadata.Preset +
      +
    getNextPosition() - +Method in class compbio.metadata.ChunkHolder +
      +
    getNumberOfSequencesAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getOnelineFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getOptionName() - +Method in class compbio.metadata.Parameter +
      +
    getOptionNames() - +Method in class compbio.metadata.Option +
      +
    getOptions() - +Method in class compbio.metadata.Preset +
      +
    getOptions() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of the Options supported by the executable of type T +
    getParameters() - +Method in class compbio.metadata.RunnerConfig +
    Returns the list of parameters supported executable of type T. +
    getPossibleValues() - +Method in interface compbio.metadata.Argument +
      +
    getPossibleValues() - +Method in class compbio.metadata.Option +
    List of possible optionNames +
    getPossibleValues() - +Method in class compbio.metadata.Parameter +
    List is more convenient to work with +
    getPreset() - +Method in class compbio.metadata.Limit +
      +
    getPresetByName(String) - +Method in class compbio.metadata.PresetManager +
      +
    getPresets() - +Method in interface compbio.data.msa.MsaWS +
    Get presets supported by a web service +
    getPresets() - +Method in class compbio.metadata.PresetManager +
      +
    getPrmSeparator() - +Method in class compbio.metadata.RunnerConfig +
      +
    getProgram() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getResult(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the result of the job. +
    getRunnerClassName() - +Method in class compbio.metadata.PresetManager +
      +
    getRunnerClassName() - +Method in class compbio.metadata.RunnerConfig +
      +
    getRunnerOptions() - +Method in interface compbio.data.msa.MsaWS +
    Get options supported by a web service +
    getSeqNumber() - +Method in class compbio.metadata.Limit +
      +
    getSequence() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of sequence +
    getSequenceLenghtActual() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequenceLenghtAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequences() - +Method in class compbio.data.sequence.Alignment +
      +
    getService(String) - +Static method in enum compbio.ws.client.Services +
      +
    getService(Class) - +Static method in enum compbio.ws.client.Services +
      +
    getServiceName(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts service name from the command line +
    getSize() - +Method in class compbio.data.sequence.Alignment +
      +
    getType() - +Method in class compbio.metadata.ValueConstrain +
      +
    getValidValue() - +Method in class compbio.metadata.Parameter +
      +
    +
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    hashCode() - +Method in class compbio.data.sequence.Alignment +
      +
    hashCode() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    hashCode() - +Method in class compbio.data.sequence.FastaSequence +
      +
    hashCode() - +Method in class compbio.metadata.ChunkHolder +
      +
    hashCode() - +Method in class compbio.metadata.Limit +
      +
    hashCode() - +Method in class compbio.metadata.Option +
      +
    hashCode() - +Method in class compbio.metadata.Parameter +
      +
    hashCode() - +Method in class compbio.metadata.Preset +
      +
    hashCode() - +Method in class compbio.metadata.ValueConstrain +
      +
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    isAmbiguosProtein(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Check whether the sequence confirms to amboguous protein sequence +
    isDefault() - +Method in class compbio.metadata.Limit +
      +
    isExceeded(List<FastaSequence>) - +Method in class compbio.metadata.Limit +
    Checks if the number of sequences or their average length in the dataset + exceeds this limit. +
    isNonAmbNucleotideSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +
    isNucleotideSequence(FastaSequence) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isProteinSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isRequired - +Variable in class compbio.metadata.Option +
      +
    isRequired() - +Method in class compbio.metadata.Option +
    Flag that indicated that this option must be specified in the command + line for an executable to run +
    isValidClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Please note this method closes the input stream provided as a parameter +
    +
    + + + + + + + + + + + + + + + +
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    +
    +
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobExecutionException(String) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(String, Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(String, Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    Jws2Client - Class in compbio.ws.client
    A command line client for JAva Bioinformatics Analysis Web Services
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Packages
    compbio.data.msaWeb Service interfaces for JAva Bioinformatics Analysis Web Services.
    compbio.data.sequenceA data model for multiple sequence alignment web services and utility methods + that work on the objects of this model.
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    compbio.ws.clientA command line client and web services testing client for + JAva Bioinformatics Analysis Web Services.
    + +

    + 

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    +Hierarchy For All Packages

    +
    +
    +
    Package Hierarchies:
    compbio.data.msa, compbio.data.sequence, compbio.metadata, compbio.ws.client
    +
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    +Serialized Form

    +
    +
    + + + + + +
    +Package compbio.data.sequence
    + +

    + + + + + +
    +Class compbio.data.sequence.UnknownFileFormatException extends Exception implements Serializable
    + +

    +serialVersionUID: 196629543695636854L + +

    + + + + + +
    +Serialized Fields
    + +

    +file

    +
    +File file
    +
    +
    +
    +
    +
    + + + + + +
    +Package compbio.metadata
    + +

    + + + + + +
    +Class compbio.metadata.JobExecutionException extends Exception implements Serializable
    + +

    +serialVersionUID: -5477751361755778769L + +

    + +

    + + + + + +
    +Class compbio.metadata.JobSubmissionException extends Exception implements Serializable
    + +

    +serialVersionUID: 607986894357895572L + +

    + +

    + + + + + +
    +Class compbio.metadata.LimitExceededException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: 15066952180013505L + +

    + + + + + +
    +Serialized Fields
    + +

    +numberOfSequencesAllowed

    +
    +int numberOfSequencesAllowed
    +
    +
    +
    +
    +
    +

    +actualNumberofSequences

    +
    +int actualNumberofSequences
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtAllowed

    +
    +int aSequenceLenghtAllowed
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtActual

    +
    +int aSequenceLenghtActual
    +
    +
    +
    +
    + +

    + + + + + +
    +Class compbio.metadata.ResultNotAvailableException extends Exception implements Serializable
    + +

    +serialVersionUID: -5475613614578761L + +

    + +

    + + + + + +
    +Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: -86624836785110293L + +

    + +

    + + + + + +
    +Class compbio.metadata.WrongParameterException extends Exception implements Serializable
    + +

    +serialVersionUID: -547775417557345769L + +

    + +

    +

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    + + + +
    + + + +
    +

    For Users

    +

    JABAWS Server Virtual Machine

    +

    JABAWS virtual machine is a way of running fully functional JABA Web Services on your own computer. To use virtual machine (VM) you have to install a software for running it. We would recommend VMWare Player v 3.1 for Windows and Linux users. There is also an Oracle VirtualBox v. 3.2 for Mac users. Both are free and installation is simple. Jalview can use your local JABAWS VM.

    +
      +
    • JABAWS Virtual Appliance: download (520M)
      • +
    +

    Please check out our manual for the detailed instructions.

    +

    For System Administrators

    +

    JABAWS Server Web Application

    +

    The JABAWS Server Web Application aRchive (WAR) version is for you if you want to deploy JABAWS for many users e.g. your laboratory or if you are an expert user and want to have more control on JABAWS. Typically, you will have a cluster or at least a powerful server machine which all users are willing to use. If you only have a single server then, you may use JABAWS Server Virtual Appliance instead. The server is provided as a self-contained Web Application +aRchive (WAR) containing all necessary binaries. WAR file can be deployed on any + web application server +supporting Servlet 2.4 specification i.e. Tomcat 6.0.

    + +
      +
    • A Complete Server for all platforms: download +(45M)
      • +
    + + +

    Please bear in mind that if you deploy JABAWS WAR on Windows only Muscle and Clustal web services will work! If you want to run other web services on Windows use JABAWS Server VM package instead. + +

    +

    For Bioinformaticians/Developers

    +

    JABAWS Command Line Client

    +

    The command line client is an executable Java program for scripting against JABA web services. If you intend to use JABAWS in your own program and need a template - download a command line client source package. You can even generate a Graphical User Interface (GUI) for JABA web services for your own program! You can consult Jalview source code for a help with that.

    +
      +
    • Command line client + +
      • +
    +

    Help with a command line client is available from the manual pages.

    + +
    + + + + + +
    + + + +
    + + +
    + + + +
    + + + diff --git a/website/full_javadoc/allclasses-frame.html b/website/full_javadoc/allclasses-frame.html new file mode 100644 index 0000000..16054f8 --- /dev/null +++ b/website/full_javadoc/allclasses-frame.html @@ -0,0 +1,309 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
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    +
    + + + diff --git a/website/full_javadoc/allclasses-noframe.html b/website/full_javadoc/allclasses-noframe.html new file mode 100644 index 0000000..bad8588 --- /dev/null +++ b/website/full_javadoc/allclasses-noframe.html @@ -0,0 +1,309 @@ + + + + + + +All Classes + + + + + + + + + + + +All Classes +
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    Align +
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    +BlastAll +
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    +BlastParser +
    +CancelJob +
    +CancelJobResponse +
    +ChunkHolder +
    +Cleaner +
    +ClustalAlignmentUtil +
    +ClustalW +
    +ClustalWS +
    +ClusterJobId +
    +ClusterNativeSpecExecutable +
    +ClusterSession +
    +ClusterUtil +
    +CommandBuilder +
    +ConfExecutable +
    +Configurator +
    +ConfiguredExecutable +
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    +CustomAlignResponse +
    +DirectoryManager +
    +Disembl +
    +Environment +
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    +ExecutableWrapper +
    +FastaSequence +
    +FilePuller +
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    +GetJobStatusResponse +
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    +GetPresetsResponse +
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    +JnetAnnotation +
    +Job +
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    +JobExecutionExceptionBean +
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    +JobSubmissionExceptionBean +
    +Jpred4 +
    +JpredAnnotation +
    +JpredResult +
    +Jws2Client +
    +Jws2Client.Services +
    +Limit +
    +LimitExceededException +
    +LimitExceededExceptionBean +
    +LimitsManager +
    +LoadBalancer +
    +LocalEngineUtil +
    +LocalExecutorService +
    +LocalRunner +
    +Mafft +
    +MafftWS +
    +Mcl +
    +MsaWS +
    +Muscle +
    +MuscleWS +
    +NetNglyc +
    +OB +
    +Option +
    +OptionCombinator +
    +Pairwise +
    +Parameter +
    +PathValidator +
    +PipedExecutable +
    +Preset +
    +PresetAlign +
    +PresetAlignResponse +
    +PresetManager +
    +Probcons +
    +ProbconsWS +
    +Program +
    +ProgressGetter +
    +PropertyHelperManager +
    +PScore +
    +PSIBlast +
    +PsiBlast +
    +PulledFileCache +
    +PullExecStatistics +
    +PullExecStatisticsResponse +
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    +Util +
    +ValueConstrain +
    +ValueConstrain.Type +
    +WrongParameterException +
    +WrongParameterExceptionBean +
    +WSTester +
    +WSUtil +
    +_DrmaaExample +
    +_JobStatus +
    +_Jpred +
    +_Key +
    +_NativeSpecHelper +
    +_Queue +
    +_QueueConstraints +
    +_SkeletalCommandBuilder +
    +_TrackingExecutor +
    +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html new file mode 100644 index 0000000..7afbc88 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JnetAnnotation.html @@ -0,0 +1,418 @@ + + + + + + +JnetAnnotation + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.data._structure +
    +Enum JnetAnnotation

    +
    +java.lang.Object
+  extended by java.lang.Enum<JnetAnnotation>
+      extended by compbio.data._structure.JnetAnnotation
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<JnetAnnotation>
    +
    +
    +
    +
    public enum JnetAnnotation
    extends java.lang.Enum<JnetAnnotation>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    JNETCONF + +
    +           
    JNETHMM + +
    +           
    jnetpred + +
    +           
    JNETPROPE + +
    +           
    JNETPROPH + +
    +           
    JNETSOL0 + +
    +           
    JNETSOL25 + +
    +           
    JNETSOL5 + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static JnetAnnotationvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JnetAnnotation[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +jnetpred

    +
    +public static final JnetAnnotation jnetpred
    +
    +
    +
    +
    +
    + +

    +JNETCONF

    +
    +public static final JnetAnnotation JNETCONF
    +
    +
    +
    +
    +
    + +

    +JNETSOL25

    +
    +public static final JnetAnnotation JNETSOL25
    +
    +
    +
    +
    +
    + +

    +JNETSOL5

    +
    +public static final JnetAnnotation JNETSOL5
    +
    +
    +
    +
    +
    + +

    +JNETSOL0

    +
    +public static final JnetAnnotation JNETSOL0
    +
    +
    +
    +
    +
    + +

    +JNETHMM

    +
    +public static final JnetAnnotation JNETHMM
    +
    +
    +
    +
    +
    + +

    +JNETPROPH

    +
    +public static final JnetAnnotation JNETPROPH
    +
    +
    +
    +
    +
    + +

    +JNETPROPE

    +
    +public static final JnetAnnotation JNETPROPE
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static JnetAnnotation[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (JnetAnnotation c : JnetAnnotation.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static JnetAnnotation valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html new file mode 100644 index 0000000..d72000f --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JpredAnnotation.html @@ -0,0 +1,418 @@ + + + + + + +JpredAnnotation + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.data._structure +
    +Enum JpredAnnotation

    +
    +java.lang.Object
+  extended by java.lang.Enum<JpredAnnotation>
+      extended by compbio.data._structure.JpredAnnotation
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<JpredAnnotation>
    +
    +
    +
    +
    public enum JpredAnnotation
    extends java.lang.Enum<JpredAnnotation>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    JNETCONF + +
    +           
    JNETHMM + +
    +           
    jnetpred + +
    +           
    JNETPROPE + +
    +           
    JNETPROPH + +
    +           
    JNETSOL0 + +
    +           
    JNETSOL25 + +
    +           
    JNETSOL5 + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static JpredAnnotationvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JpredAnnotation[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +jnetpred

    +
    +public static final JpredAnnotation jnetpred
    +
    +
    +
    +
    +
    + +

    +JNETCONF

    +
    +public static final JpredAnnotation JNETCONF
    +
    +
    +
    +
    +
    + +

    +JNETSOL25

    +
    +public static final JpredAnnotation JNETSOL25
    +
    +
    +
    +
    +
    + +

    +JNETSOL5

    +
    +public static final JpredAnnotation JNETSOL5
    +
    +
    +
    +
    +
    + +

    +JNETSOL0

    +
    +public static final JpredAnnotation JNETSOL0
    +
    +
    +
    +
    +
    + +

    +JNETHMM

    +
    +public static final JpredAnnotation JNETHMM
    +
    +
    +
    +
    +
    + +

    +JNETPROPH

    +
    +public static final JpredAnnotation JNETPROPH
    +
    +
    +
    +
    +
    + +

    +JNETPROPE

    +
    +public static final JpredAnnotation JNETPROPE
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static JpredAnnotation[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (JpredAnnotation c : JpredAnnotation.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static JpredAnnotation valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/JpredResult.html b/website/full_javadoc/compbio/data/_structure/JpredResult.html new file mode 100644 index 0000000..904c222 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/JpredResult.html @@ -0,0 +1,260 @@ + + + + + + +JpredResult + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data._structure +
    +Class JpredResult

    +
    +java.lang.Object
+  extended by compbio.data._structure.JpredResult
+
    +
    +
    +
    public class JpredResult
    extends java.lang.Object
    + + +

    +Jnet result + + jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H + ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, + -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- + , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 + 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 + , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- + , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- + ,B, + JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- + ,-,- + JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, + -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, + JNETHMM:-,H,H,H,H,H,H,H,H,H,H, + H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,- + ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, + JNETPROPH:0.0110,0.1125,0.8552,0.0107 + ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 + ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 + ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, + JNETPROPE:0.0107,0.6245,0.3614,0.0120 + ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 + ,0.9586,0.0465,0.0094,0.9662,0.0433, + ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784, +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    JpredResult() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JpredResult

    +
    +public JpredResult()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html new file mode 100644 index 0000000..db95c3b --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JnetAnnotation.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data._structure.JnetAnnotation + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data._structure.JnetAnnotation

    +
    + + + + + + + + + +
    +Packages that use JnetAnnotation
    compbio.data._structure  
    +  +

    + + + + + +
    +Uses of JnetAnnotation in compbio.data._structure
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data._structure that return JnetAnnotation
    +static JnetAnnotationJnetAnnotation.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JnetAnnotation[]JnetAnnotation.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html new file mode 100644 index 0000000..fcae915 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JpredAnnotation.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Class compbio.data._structure.JpredAnnotation + + + + + + + + + + + + +
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    +Uses of Class
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    +
    + + + + + + + + + +
    +Packages that use JpredAnnotation
    compbio.data._structure  
    +  +

    + + + + + +
    +Uses of JpredAnnotation in compbio.data._structure
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data._structure that return JpredAnnotation
    +static JpredAnnotationJpredAnnotation.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JpredAnnotation[]JpredAnnotation.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html b/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html new file mode 100644 index 0000000..8366955 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/class-use/JpredResult.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data._structure.JpredResult + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data._structure.JpredResult

    +
    +No usage of compbio.data._structure.JpredResult +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/_structure/package-frame.html b/website/full_javadoc/compbio/data/_structure/package-frame.html new file mode 100644 index 0000000..aef6a7c --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/package-frame.html @@ -0,0 +1,45 @@ + + + + + + +compbio.data._structure + + + + + + + + + + + +compbio.data._structure + + + + +
    +Classes  + +
    +JpredResult
    + + + + + + +
    +Enums  + +
    +JnetAnnotation +
    +JpredAnnotation
    + + + + diff --git a/website/full_javadoc/compbio/data/_structure/package-summary.html b/website/full_javadoc/compbio/data/_structure/package-summary.html new file mode 100644 index 0000000..9f34326 --- /dev/null +++ b/website/full_javadoc/compbio/data/_structure/package-summary.html @@ -0,0 +1,203 @@ + + + + + + +compbio.data._structure + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +

    +Package compbio.data._structure +

    + + + + + + + + + +
    +Class Summary
    JpredResultJnet result + + jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H + ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, + -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- + , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 + 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 + , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- + , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- + ,B, + JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- + ,-,- + JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, + -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, + JNETHMM:-,H,H,H,H,H,H,H,H,H,H, + H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,- + ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, + JNETPROPH:0.0110,0.1125,0.8552,0.0107 + ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 + ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 + ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, + JNETPROPE:0.0107,0.6245,0.3614,0.0120 + ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 + ,0.9586,0.0465,0.0094,0.9662,0.0433, + ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    +  + +

    + + + + + + + + + + + + + +
    +Enum Summary
    JnetAnnotation 
    JpredAnnotation 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.data._structure +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    +
      +
    • java.lang.Object +
    +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    +Uses of Package
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    +
    + + + + + + + + + +
    +Packages that use compbio.data._structure
    compbio.data._structure  
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.data._structure used by compbio.data._structure
    JnetAnnotation + +
    +           
    JpredAnnotation + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/MsaWS.html b/website/full_javadoc/compbio/data/msa/MsaWS.html new file mode 100644 index 0000000..911f90d --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/MsaWS.html @@ -0,0 +1,567 @@ + + + + + + +MsaWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa +
    +Interface MsaWS<T>

    +
    +
    Type Parameters:
    T - executable type / web service type
    +
    +
    All Known Implementing Classes:
    ClustalWS, MafftWS, MuscleWS, ProbconsWS, TcoffeeWS
    +
    +
    +
    +
    public interface MsaWS<T>
    + + +

    +Multiple Sequence Alignment (MSA) Web Services Interface +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<T>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<T>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<T>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<T>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws UnsupportedRuntimeException,
+                              LimitExceededException,
+                              JobSubmissionException
    +
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    JobSubmissionException. - This + exception is thrown when the job could not be submitted due + to the following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
    java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                             java.util.List<Option<T>> options)
+                             throws UnsupportedRuntimeException,
+                                    LimitExceededException,
+                                    JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Align a list of sequences with options. +

    +

    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    JobSubmissionException. - This + exception is thrown when the job could not be submitted due + to the following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                             Preset<T> preset)
+                             throws UnsupportedRuntimeException,
+                                    LimitExceededException,
+                                    JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    JobSubmissionException. - This + exception is thrown when the job could not be submitted due + to the following reasons: 1) The number of sequences in the + submission or their average length is greater then defined by + the default Limit. 2) Any problems on the server side e.g. it + is misconfigured or malfunction, is reported via this + exception. In the first case the information on the limit + could be obtained from an exception. +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    java.security.InvalidParameterException - thrown if input list of fasta sequence is null or empty +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JABAWS is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Return the result of the job. +

    +

    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException. +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
    +
    +
    +
    + +

    +cancelJob

    +
    +boolean cancelJob(java.lang.String jobId)
    +
    +
    Stop running job but leave its output untouched +

    +

    + +
    Returns:
    true if job was cancelled successfully, false otherwise +
    Throws: +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
    +
    +
    +
    + +

    +getJobStatus

    +
    +JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job +
    Throws: +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +ChunkHolder pullExecStatistics(java.lang.String jobId,
+                               long position)
    +
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read +
    Throws: +
    java.security.InvalidParameterException - thrown if jobId is empty or cannot be recognised e.g. in + invalid format and also if the position value is negative
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +RunnerConfig<T> getRunnerOptions()
    +
    +
    Get options supported by a web service +

    +

    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    +
    + +

    +getPresets

    +
    +PresetManager<T> getPresets()
    +
    +
    Get presets supported by a web service +

    +

    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getLimit

    +
    +Limit<T> getLimit(java.lang.String presetName)
    +
    +
    Get a Limit for a preset. +

    +

    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +LimitsManager<T> getLimits()
    +
    +
    List Limits supported by a web service. +

    +

    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    LimitManager
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html new file mode 100644 index 0000000..30ccaec --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/class-use/MsaWS.html @@ -0,0 +1,249 @@ + + + + + + +Uses of Interface compbio.data.msa.MsaWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.data.msa.MsaWS

    +
    + + + + + + + + + + + + + +
    +Packages that use MsaWS
    compbio.ws.client  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of MsaWS in compbio.ws.client
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client that return MsaWS
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

    + + + + + +
    +Uses of MsaWS in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Classes in compbio.ws.server that implement MsaWS
    + classClustalWS + +
    +           
    + classMafftWS + +
    +           
    + classMuscleWS + +
    +           
    + classProbconsWS + +
    +           
    + classTcoffeeWS + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/Align.html new file mode 100644 index 0000000..b4181e3 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/Align.html @@ -0,0 +1,272 @@ + + + + + + +Align + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class Align

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.Align
+
    +
    +
    +
    public class Align
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Align() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Align

    +
    +public Align()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getFastaSequences

    +
    +public java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

    +
    +public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
    +
    +
    +
    Parameters:
    fastaSequences - the value for the fastaSequences property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html new file mode 100644 index 0000000..1a50071 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/AlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +AlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class AlignResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.AlignResponse
+
    +
    +
    +
    public class AlignResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AlignResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetReturn() + +
    +           
    + voidsetReturn(java.lang.String _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +AlignResponse

    +
    +public AlignResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.String _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html new file mode 100644 index 0000000..e858d81 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CancelJob.html @@ -0,0 +1,272 @@ + + + + + + +CancelJob + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class CancelJob

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.CancelJob
+
    +
    +
    +
    public class CancelJob
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CancelJob() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CancelJob

    +
    +public CancelJob()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html new file mode 100644 index 0000000..69785d5 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CancelJobResponse.html @@ -0,0 +1,272 @@ + + + + + + +CancelJobResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class CancelJobResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.CancelJobResponse
+
    +
    +
    +
    public class CancelJobResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CancelJobResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanisReturn() + +
    +           
    + voidsetReturn(boolean _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CancelJobResponse

    +
    +public CancelJobResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +isReturn

    +
    +public boolean isReturn()
    +
    +
    + +
    Returns:
    returns boolean
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(boolean _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html new file mode 100644 index 0000000..838e512 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlign.html @@ -0,0 +1,311 @@ + + + + + + +CustomAlign + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class CustomAlign

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.CustomAlign
+
    +
    +
    +
    public class CustomAlign
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CustomAlign() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + java.util.List<Option>getOptions() + +
    +           
    + voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidsetOptions(java.util.List<Option> options) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CustomAlign

    +
    +public CustomAlign()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getFastaSequences

    +
    +public java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

    +
    +public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
    +
    +
    +
    Parameters:
    fastaSequences - the value for the fastaSequences property
    +
    +
    +
    + +

    +getOptions

    +
    +public java.util.List<Option> getOptions()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setOptions

    +
    +public void setOptions(java.util.List<Option> options)
    +
    +
    +
    Parameters:
    options - the value for the options property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html new file mode 100644 index 0000000..a7d5cfe --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/CustomAlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +CustomAlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class CustomAlignResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.CustomAlignResponse
+
    +
    +
    +
    public class CustomAlignResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CustomAlignResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetReturn() + +
    +           
    + voidsetReturn(java.lang.String _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CustomAlignResponse

    +
    +public CustomAlignResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.String _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html new file mode 100644 index 0000000..e4f1719 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatus.html @@ -0,0 +1,272 @@ + + + + + + +GetJobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetJobStatus

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetJobStatus
+
    +
    +
    +
    public class GetJobStatus
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetJobStatus() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetJobStatus

    +
    +public GetJobStatus()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html new file mode 100644 index 0000000..401d145 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetJobStatusResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetJobStatusResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetJobStatusResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetJobStatusResponse
+
    +
    +
    +
    public class GetJobStatusResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetJobStatusResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + JobStatusgetReturn() + +
    +           
    + voidsetReturn(JobStatus _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetJobStatusResponse

    +
    +public GetJobStatusResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public JobStatus getReturn()
    +
    +
    + +
    Returns:
    returns JobStatus
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(JobStatus _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html new file mode 100644 index 0000000..3433200 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimit.html @@ -0,0 +1,272 @@ + + + + + + +GetLimit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetLimit

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimit
+
    +
    +
    +
    public class GetLimit
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetLimit() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetPresetName() + +
    +           
    + voidsetPresetName(java.lang.String presetName) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetLimit

    +
    +public GetLimit()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPresetName

    +
    +public java.lang.String getPresetName()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setPresetName

    +
    +public void setPresetName(java.lang.String presetName)
    +
    +
    +
    Parameters:
    presetName - the value for the presetName property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html new file mode 100644 index 0000000..5def54c --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetLimitResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetLimitResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimitResponse
+
    +
    +
    +
    public class GetLimitResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetLimitResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + LimitgetReturn() + +
    +           
    + voidsetReturn(Limit _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetLimitResponse

    +
    +public GetLimitResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public Limit getReturn()
    +
    +
    + +
    Returns:
    returns Limit
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(Limit _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html new file mode 100644 index 0000000..aa83b59 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimits.html @@ -0,0 +1,224 @@ + + + + + + +GetLimits + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetLimits

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimits
+
    +
    +
    +
    public class GetLimits
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetLimits() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetLimits

    +
    +public GetLimits()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html new file mode 100644 index 0000000..04d2e7a --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetLimitsResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetLimitsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetLimitsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetLimitsResponse
+
    +
    +
    +
    public class GetLimitsResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetLimitsResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + LimitsManagergetReturn() + +
    +           
    + voidsetReturn(LimitsManager _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetLimitsResponse

    +
    +public GetLimitsResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public LimitsManager getReturn()
    +
    +
    + +
    Returns:
    returns LimitsManager
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(LimitsManager _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html new file mode 100644 index 0000000..a9ea45a --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetPresets.html @@ -0,0 +1,224 @@ + + + + + + +GetPresets + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetPresets

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetPresets
+
    +
    +
    +
    public class GetPresets
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetPresets() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetPresets

    +
    +public GetPresets()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html new file mode 100644 index 0000000..f5f62bb --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetPresetsResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetPresetsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetPresetsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetPresetsResponse
+
    +
    +
    +
    public class GetPresetsResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetPresetsResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + PresetManagergetReturn() + +
    +           
    + voidsetReturn(PresetManager _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetPresetsResponse

    +
    +public GetPresetsResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public PresetManager getReturn()
    +
    +
    + +
    Returns:
    returns PresetManager
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(PresetManager _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html new file mode 100644 index 0000000..97f3af9 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetProgress.html @@ -0,0 +1,272 @@ + + + + + + +GetProgress + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetProgress

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetProgress
+
    +
    +
    +
    public class GetProgress
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetProgress() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetProgress

    +
    +public GetProgress()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html new file mode 100644 index 0000000..0f30084 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetProgressResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetProgressResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetProgressResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetProgressResponse
+
    +
    +
    +
    public class GetProgressResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetProgressResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + bytegetReturn() + +
    +           
    + voidsetReturn(byte _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetProgressResponse

    +
    +public GetProgressResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public byte getReturn()
    +
    +
    + +
    Returns:
    returns byte
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(byte _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html new file mode 100644 index 0000000..c4e3b36 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetResult.html @@ -0,0 +1,272 @@ + + + + + + +GetResult + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetResult

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetResult
+
    +
    +
    +
    public class GetResult
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetResult() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetResult

    +
    +public GetResult()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html new file mode 100644 index 0000000..e5da690 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetResultResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetResultResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetResultResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetResultResponse
+
    +
    +
    +
    public class GetResultResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetResultResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + AlignmentgetReturn() + +
    +           
    + voidsetReturn(Alignment _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetResultResponse

    +
    +public GetResultResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public Alignment getReturn()
    +
    +
    + +
    Returns:
    returns Alignment
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(Alignment _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html new file mode 100644 index 0000000..e3125c6 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptions.html @@ -0,0 +1,224 @@ + + + + + + +GetRunnerOptions + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetRunnerOptions

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetRunnerOptions
+
    +
    +
    +
    public class GetRunnerOptions
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetRunnerOptions() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetRunnerOptions

    +
    +public GetRunnerOptions()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html new file mode 100644 index 0000000..ddc4c44 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/GetRunnerOptionsResponse.html @@ -0,0 +1,272 @@ + + + + + + +GetRunnerOptionsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class GetRunnerOptionsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.GetRunnerOptionsResponse
+
    +
    +
    +
    public class GetRunnerOptionsResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    GetRunnerOptionsResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + RunnerConfiggetReturn() + +
    +           
    + voidsetReturn(RunnerConfig _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +GetRunnerOptionsResponse

    +
    +public GetRunnerOptionsResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public RunnerConfig getReturn()
    +
    +
    + +
    Returns:
    returns RunnerConfig
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(RunnerConfig _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html new file mode 100644 index 0000000..90a42af --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/JobExecutionExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +JobExecutionExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class JobExecutionExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.JobExecutionExceptionBean
+
    +
    +
    +
    public class JobExecutionExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    JobExecutionExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobExecutionExceptionBean

    +
    +public JobExecutionExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html new file mode 100644 index 0000000..53f43dd --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/JobSubmissionExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +JobSubmissionExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class JobSubmissionExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.JobSubmissionExceptionBean
+
    +
    +
    +
    public class JobSubmissionExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    JobSubmissionExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobSubmissionExceptionBean

    +
    +public JobSubmissionExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html new file mode 100644 index 0000000..301ea94 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/LimitExceededExceptionBean.html @@ -0,0 +1,434 @@ + + + + + + +LimitExceededExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class LimitExceededExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.LimitExceededExceptionBean
+
    +
    +
    +
    public class LimitExceededExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitExceededExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetActualNumberofSequences() + +
    +           
    + java.lang.StringgetMessage() + +
    +           
    + intgetNumberOfSequencesAllowed() + +
    +           
    + intgetSequenceLenghtActual() + +
    +           
    + intgetSequenceLenghtAllowed() + +
    +           
    + voidsetActualNumberofSequences(int actualNumberofSequences) + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    + voidsetNumberOfSequencesAllowed(int numberOfSequencesAllowed) + +
    +           
    + voidsetSequenceLenghtActual(int sequenceLenghtActual) + +
    +           
    + voidsetSequenceLenghtAllowed(int sequenceLenghtAllowed) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +LimitExceededExceptionBean

    +
    +public LimitExceededExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getActualNumberofSequences

    +
    +public int getActualNumberofSequences()
    +
    +
    + +
    Returns:
    returns int
    +
    +
    +
    + +

    +setActualNumberofSequences

    +
    +public void setActualNumberofSequences(int actualNumberofSequences)
    +
    +
    +
    Parameters:
    actualNumberofSequences - the value for the actualNumberofSequences property
    +
    +
    +
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    +
    + +

    +getNumberOfSequencesAllowed

    +
    +public int getNumberOfSequencesAllowed()
    +
    +
    + +
    Returns:
    returns int
    +
    +
    +
    + +

    +setNumberOfSequencesAllowed

    +
    +public void setNumberOfSequencesAllowed(int numberOfSequencesAllowed)
    +
    +
    +
    Parameters:
    numberOfSequencesAllowed - the value for the numberOfSequencesAllowed property
    +
    +
    +
    + +

    +getSequenceLenghtActual

    +
    +public int getSequenceLenghtActual()
    +
    +
    + +
    Returns:
    returns int
    +
    +
    +
    + +

    +setSequenceLenghtActual

    +
    +public void setSequenceLenghtActual(int sequenceLenghtActual)
    +
    +
    +
    Parameters:
    sequenceLenghtActual - the value for the sequenceLenghtActual property
    +
    +
    +
    + +

    +getSequenceLenghtAllowed

    +
    +public int getSequenceLenghtAllowed()
    +
    +
    + +
    Returns:
    returns int
    +
    +
    +
    + +

    +setSequenceLenghtAllowed

    +
    +public void setSequenceLenghtAllowed(int sequenceLenghtAllowed)
    +
    +
    +
    Parameters:
    sequenceLenghtAllowed - the value for the sequenceLenghtAllowed property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html new file mode 100644 index 0000000..57cf5af --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlign.html @@ -0,0 +1,311 @@ + + + + + + +PresetAlign + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PresetAlign

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PresetAlign
+
    +
    +
    +
    public class PresetAlign
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PresetAlign() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<FastaSequence>getFastaSequences() + +
    +           
    + PresetgetPreset() + +
    +           
    + voidsetFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidsetPreset(Preset preset) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PresetAlign

    +
    +public PresetAlign()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getFastaSequences

    +
    +public java.util.List<FastaSequence> getFastaSequences()
    +
    +
    + +
    Returns:
    returns List
    +
    +
    +
    + +

    +setFastaSequences

    +
    +public void setFastaSequences(java.util.List<FastaSequence> fastaSequences)
    +
    +
    +
    Parameters:
    fastaSequences - the value for the fastaSequences property
    +
    +
    +
    + +

    +getPreset

    +
    +public Preset getPreset()
    +
    +
    + +
    Returns:
    returns Preset
    +
    +
    +
    + +

    +setPreset

    +
    +public void setPreset(Preset preset)
    +
    +
    +
    Parameters:
    preset - the value for the preset property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html new file mode 100644 index 0000000..318712e --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PresetAlignResponse.html @@ -0,0 +1,272 @@ + + + + + + +PresetAlignResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PresetAlignResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PresetAlignResponse
+
    +
    +
    +
    public class PresetAlignResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PresetAlignResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetReturn() + +
    +           
    + voidsetReturn(java.lang.String _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PresetAlignResponse

    +
    +public PresetAlignResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public java.lang.String getReturn()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(java.lang.String _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html new file mode 100644 index 0000000..1ab6ead --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatistics.html @@ -0,0 +1,311 @@ + + + + + + +PullExecStatistics + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullExecStatistics

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullExecStatistics
+
    +
    +
    +
    public class PullExecStatistics
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PullExecStatistics() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + longgetPosition() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    + voidsetPosition(long position) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullExecStatistics

    +
    +public PullExecStatistics()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    +
    + +

    +getPosition

    +
    +public long getPosition()
    +
    +
    + +
    Returns:
    returns long
    +
    +
    +
    + +

    +setPosition

    +
    +public void setPosition(long position)
    +
    +
    +
    Parameters:
    position - the value for the position property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html new file mode 100644 index 0000000..a5658d1 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullExecStatisticsResponse.html @@ -0,0 +1,272 @@ + + + + + + +PullExecStatisticsResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullExecStatisticsResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullExecStatisticsResponse
+
    +
    +
    +
    public class PullExecStatisticsResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PullExecStatisticsResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + ChunkHoldergetReturn() + +
    +           
    + voidsetReturn(ChunkHolder _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullExecStatisticsResponse

    +
    +public PullExecStatisticsResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public ChunkHolder getReturn()
    +
    +
    + +
    Returns:
    returns ChunkHolder
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(ChunkHolder _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html new file mode 100644 index 0000000..ff92d78 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullFile.html @@ -0,0 +1,311 @@ + + + + + + +PullFile + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullFile

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullFile
+
    +
    +
    +
    public class PullFile
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PullFile() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetJobId() + +
    +           
    + longgetPosition() + +
    +           
    + voidsetJobId(java.lang.String jobId) + +
    +           
    + voidsetPosition(long position) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullFile

    +
    +public PullFile()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setJobId

    +
    +public void setJobId(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - the value for the jobId property
    +
    +
    +
    + +

    +getPosition

    +
    +public long getPosition()
    +
    +
    + +
    Returns:
    returns long
    +
    +
    +
    + +

    +setPosition

    +
    +public void setPosition(long position)
    +
    +
    +
    Parameters:
    position - the value for the position property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html new file mode 100644 index 0000000..966917b --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/PullFileResponse.html @@ -0,0 +1,272 @@ + + + + + + +PullFileResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class PullFileResponse

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.PullFileResponse
+
    +
    +
    +
    public class PullFileResponse
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PullFileResponse() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + ChunkHoldergetReturn() + +
    +           
    + voidsetReturn(ChunkHolder _return) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PullFileResponse

    +
    +public PullFileResponse()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getReturn

    +
    +public ChunkHolder getReturn()
    +
    +
    + +
    Returns:
    returns ChunkHolder
    +
    +
    +
    + +

    +setReturn

    +
    +public void setReturn(ChunkHolder _return)
    +
    +
    +
    Parameters:
    _return - the value for the _return property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html new file mode 100644 index 0000000..9f89492 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +ResultNotAvailableExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class ResultNotAvailableExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.ResultNotAvailableExceptionBean
+
    +
    +
    +
    public class ResultNotAvailableExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ResultNotAvailableExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ResultNotAvailableExceptionBean

    +
    +public ResultNotAvailableExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html new file mode 100644 index 0000000..1660fdf --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +UnsupportedRuntimeExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class UnsupportedRuntimeExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean
+
    +
    +
    +
    public class UnsupportedRuntimeExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    UnsupportedRuntimeExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnsupportedRuntimeExceptionBean

    +
    +public UnsupportedRuntimeExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html new file mode 100644 index 0000000..ecf51ab --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/WrongParameterExceptionBean.html @@ -0,0 +1,278 @@ + + + + + + +WrongParameterExceptionBean + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.msa.jaxws +
    +Class WrongParameterExceptionBean

    +
    +java.lang.Object
+  extended by compbio.data.msa.jaxws.WrongParameterExceptionBean
+
    +
    +
    +
    public class WrongParameterExceptionBean
    extends java.lang.Object
    + + +

    +This class was generated by the JAX-WS RI. + JAX-WS RI 2.1.7-hudson-48- + Generated source version: 2.1.7 +

    + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterExceptionBean() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetMessage() + +
    +           
    + voidsetMessage(java.lang.String message) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WrongParameterExceptionBean

    +
    +public WrongParameterExceptionBean()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getMessage

    +
    +public java.lang.String getMessage()
    +
    +
    + +
    Returns:
    returns String
    +
    +
    +
    + +

    +setMessage

    +
    +public void setMessage(java.lang.String message)
    +
    +
    +
    Parameters:
    message - the value for the message property
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html new file mode 100644 index 0000000..63a3520 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/Align.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.Align + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
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    +

    +Uses of Class
    compbio.data.msa.jaxws.Align

    +
    +No usage of compbio.data.msa.jaxws.Align +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/AlignResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/AlignResponse.html new file mode 100644 index 0000000..5cbfb3c --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/AlignResponse.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.AlignResponse + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.data.msa.jaxws.AlignResponse

    +
    +No usage of compbio.data.msa.jaxws.AlignResponse +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html new file mode 100644 index 0000000..2c0d93c --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJob.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.CancelJob + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.data.msa.jaxws.CancelJob

    +
    +No usage of compbio.data.msa.jaxws.CancelJob +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJobResponse.html b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJobResponse.html new file mode 100644 index 0000000..6aa2d31 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/class-use/CancelJobResponse.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.msa.jaxws.CancelJobResponse + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +
    +No usage of compbio.data.msa.jaxws.CancelJobResponse +

    +

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    compbio.data.msa.jaxws.CustomAlign

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    +No usage of compbio.data.msa.jaxws.CustomAlign +

    +

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    +

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    compbio.data.msa.jaxws.GetJobStatus

    +
    +No usage of compbio.data.msa.jaxws.GetJobStatus +

    +

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    compbio.data.msa.jaxws.GetJobStatusResponse

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    +No usage of compbio.data.msa.jaxws.GetJobStatusResponse +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetLimit

    +
    +No usage of compbio.data.msa.jaxws.GetLimit +

    +

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    compbio.data.msa.jaxws.GetLimitResponse

    +
    +No usage of compbio.data.msa.jaxws.GetLimitResponse +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetLimits

    +
    +No usage of compbio.data.msa.jaxws.GetLimits +

    +

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    +Uses of Class
    compbio.data.msa.jaxws.GetLimitsResponse

    +
    +No usage of compbio.data.msa.jaxws.GetLimitsResponse +

    +

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    compbio.data.msa.jaxws.GetPresets

    +
    +No usage of compbio.data.msa.jaxws.GetPresets +

    +

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    compbio.data.msa.jaxws.GetPresetsResponse

    +
    +No usage of compbio.data.msa.jaxws.GetPresetsResponse +

    +

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    compbio.data.msa.jaxws.GetProgress

    +
    +No usage of compbio.data.msa.jaxws.GetProgress +

    +

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    compbio.data.msa.jaxws.GetProgressResponse

    +
    +No usage of compbio.data.msa.jaxws.GetProgressResponse +

    +

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    compbio.data.msa.jaxws.GetResult

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    +No usage of compbio.data.msa.jaxws.GetResult +

    +

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    compbio.data.msa.jaxws.GetResultResponse

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    +No usage of compbio.data.msa.jaxws.GetResultResponse +

    +

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    compbio.data.msa.jaxws.GetRunnerOptions

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    +No usage of compbio.data.msa.jaxws.GetRunnerOptions +

    +

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    compbio.data.msa.jaxws.GetRunnerOptionsResponse

    +
    +No usage of compbio.data.msa.jaxws.GetRunnerOptionsResponse +

    +

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    compbio.data.msa.jaxws.JobExecutionExceptionBean

    +
    +No usage of compbio.data.msa.jaxws.JobExecutionExceptionBean +

    +

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    compbio.data.msa.jaxws.JobSubmissionExceptionBean

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    +No usage of compbio.data.msa.jaxws.JobSubmissionExceptionBean +

    +

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    +

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    +

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    +

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    +Classes  + +
    +Align +
    +AlignResponse +
    +CancelJob +
    +CancelJobResponse +
    +CustomAlign +
    +CustomAlignResponse +
    +GetJobStatus +
    +GetJobStatusResponse +
    +GetLimit +
    +GetLimitResponse +
    +GetLimits +
    +GetLimitsResponse +
    +GetPresets +
    +GetPresetsResponse +
    +GetProgress +
    +GetProgressResponse +
    +GetResult +
    +GetResultResponse +
    +GetRunnerOptions +
    +GetRunnerOptionsResponse +
    +JobExecutionExceptionBean +
    +JobSubmissionExceptionBean +
    +LimitExceededExceptionBean +
    +PresetAlign +
    +PresetAlignResponse +
    +PullExecStatistics +
    +PullExecStatisticsResponse +
    +PullFile +
    +PullFileResponse +
    +ResultNotAvailableExceptionBean +
    +UnsupportedRuntimeExceptionBean +
    +WrongParameterExceptionBean
    + + + + diff --git a/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html b/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html new file mode 100644 index 0000000..cf10084 --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/jaxws/package-summary.html @@ -0,0 +1,281 @@ + + + + + + +compbio.data.msa.jaxws + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Package compbio.data.msa.jaxws +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    Align 
    AlignResponse 
    CancelJob 
    CancelJobResponse 
    CustomAlign 
    CustomAlignResponse 
    GetJobStatus 
    GetJobStatusResponse 
    GetLimit 
    GetLimitResponse 
    GetLimits 
    GetLimitsResponse 
    GetPresets 
    GetPresetsResponse 
    GetProgress 
    GetProgressResponse 
    GetResult 
    GetResultResponse 
    GetRunnerOptions 
    GetRunnerOptionsResponse 
    JobExecutionExceptionBeanThis class was generated by the JAX-WS RI.
    JobSubmissionExceptionBeanThis class was generated by the JAX-WS RI.
    LimitExceededExceptionBeanThis class was generated by the JAX-WS RI.
    PresetAlign 
    PresetAlignResponse 
    PullExecStatistics 
    PullExecStatisticsResponse 
    PullFile 
    PullFileResponse 
    ResultNotAvailableExceptionBeanThis class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBeanThis class was generated by the JAX-WS RI.
    WrongParameterExceptionBeanThis class was generated by the JAX-WS RI.
    +  + +

    +

    +
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    + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.data.msa.jaxws +

    +
    +
    +
    Package Hierarchies:
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    +
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    +No usage of compbio.data.msa.jaxws +

    +

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    +Interfaces  + +
    +MsaWS
    + + + + diff --git a/website/full_javadoc/compbio/data/msa/package-summary.html b/website/full_javadoc/compbio/data/msa/package-summary.html new file mode 100644 index 0000000..3cb53ac --- /dev/null +++ b/website/full_javadoc/compbio/data/msa/package-summary.html @@ -0,0 +1,157 @@ + + + + + + +compbio.data.msa + + + + + + + + + + + + +
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    +Package compbio.data.msa +

    + + + + + + + + + +
    +Interface Summary
    MsaWS<T>Multiple Sequence Alignment (MSA) Web Services Interface
    +  + +

    +

    +
    +
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    +Hierarchy For Package compbio.data.msa +

    +
    +
    +
    Package Hierarchies:
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    +
    +

    +Interface Hierarchy +

    +
      +
    • compbio.data.msa.MsaWS<T>
    +
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    +Uses of Package
    compbio.data.msa

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.data.msa
    compbio.ws.client  
    compbio.ws.server  
    +  +

    + + + + + + + + +
    +Classes in compbio.data.msa used by compbio.ws.client
    MsaWS + +
    +          Multiple Sequence Alignment (MSA) Web Services Interface
    +  +

    + + + + + + + + +
    +Classes in compbio.data.msa used by compbio.ws.server
    MsaWS + +
    +          Multiple Sequence Alignment (MSA) Web Services Interface
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/Alignment.html b/website/full_javadoc/compbio/data/sequence/Alignment.html new file mode 100644 index 0000000..8cad073 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/Alignment.html @@ -0,0 +1,381 @@ + + + + + + +Alignment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class Alignment

    +
    +java.lang.Object
+  extended by compbio.data.sequence.Alignment
+
    +
    +
    +
    @Immutable
+public final class Alignment
    extends java.lang.Object
    + + +

    +Multiple sequence alignment. + + Does not give any guarantees on the content of individual FastaSequece + records. That is it does not guarantee that the neither the names of + sequences or the sequences themselves are unique. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    See Also:
    FastaSequence, +AlignmentMetadata
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    Alignment(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
    +           
    Alignment(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +          Please note that this implementation does not take the order of sequences + into account!
    + AlignmentMetadatagetMetadata() + +
    +           
    + java.util.List<FastaSequence>getSequences() + +
    +           
    + intgetSize() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Alignment

    +
    +public Alignment(java.util.List<FastaSequence> sequences,
+                 Program program,
+                 char gapchar)
    +
    +
    +
    Parameters:
    sequences -
    program -
    gapchar -
    +
    +
    + +

    +Alignment

    +
    +public Alignment(java.util.List<FastaSequence> sequences,
+                 AlignmentMetadata metadata)
    +
    +
    +
    Parameters:
    sequences -
    metadata -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getSequences

    +
    +public java.util.List<FastaSequence> getSequences()
    +
    +
    + +
    Returns:
    list of FastaSequence records
    +
    +
    +
    + +

    +getSize

    +
    +public int getSize()
    +
    +
    + +
    Returns:
    a number of sequence in the alignment
    +
    +
    +
    + +

    +getMetadata

    +
    +public AlignmentMetadata getMetadata()
    +
    +
    + +
    Returns:
    AlignmentMetadata object
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    Please note that this implementation does not take the order of sequences + into account! +

    +

    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html new file mode 100644 index 0000000..6650404 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/AlignmentMetadata.html @@ -0,0 +1,329 @@ + + + + + + +AlignmentMetadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class AlignmentMetadata

    +
    +java.lang.Object
+  extended by compbio.data.sequence.AlignmentMetadata
+
    +
    +
    +
    @Immutable
+public class AlignmentMetadata
    extends java.lang.Object
    + + +

    +Alignment metadata e.g. method/program being used to generate the alignment + and its parameters +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AlignmentMetadata(Program program, + char gapchar) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + chargetGapchar() + +
    +           
    + ProgramgetProgram() + +
    +           
    + inthashCode() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +AlignmentMetadata

    +
    +public AlignmentMetadata(Program program,
+                         char gapchar)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getProgram

    +
    +public Program getProgram()
    +
    +
    +
    +
    +
    +
    + +

    +getGapchar

    +
    +public char getGapchar()
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html new file mode 100644 index 0000000..c7fb25a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html @@ -0,0 +1,385 @@ + + + + + + +ClustalAlignmentUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class ClustalAlignmentUtil

    +
    +java.lang.Object
+  extended by compbio.data.sequence.ClustalAlignmentUtil
+
    +
    +
    +
    public final class ClustalAlignmentUtil
    extends java.lang.Object
    + + +

    +Tools to read and write clustal formated files +

    + +

    +

    +
    Author:
    +
    Petr Troshin based on jimp class + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static chargapchar + +
    +          Dash char to be used as gap char in the alignments
    +  + + + + + + + + + + +
    +Constructor Summary
    ClustalAlignmentUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleanisValidClustalFile(java.io.InputStream input) + +
    +           
    +static AlignmentreadClustalFile(java.io.File file) + +
    +           
    +static AlignmentreadClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +static voidwriteClustalAlignment(java.io.OutputStream outStream, + Alignment alignment) + +
    +          Write Clustal formatted alignment Limitations: does not record the + consensus.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +gapchar

    +
    +public static final char gapchar
    +
    +
    Dash char to be used as gap char in the alignments +

    +

    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ClustalAlignmentUtil

    +
    +public ClustalAlignmentUtil()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +readClustalFile

    +
    +public static Alignment readClustalFile(java.io.InputStream instream)
+                                 throws java.io.IOException,
+                                        UnknownFileFormatException
    +
    +
    Read Clustal formatted alignment. Limitations: Does not read consensus + + Sequence names as well as the sequences are not guaranteed to be unique! +

    +

    + +
    Throws: +
    {@link - IOException} +
    {@link - UnknownFileFormatException} +
    java.io.IOException +
    UnknownFileFormatException
    +
    +
    +
    + +

    +isValidClustalFile

    +
    +public static boolean isValidClustalFile(java.io.InputStream input)
    +
    +
    +
    Parameters:
    input - +
    Returns:
    true if the file is recognised as Clustal formatted alignment, + false otherwise
    +
    +
    +
    + +

    +writeClustalAlignment

    +
    +public static void writeClustalAlignment(java.io.OutputStream outStream,
+                                         Alignment alignment)
+                                  throws java.io.IOException
    +
    +
    Write Clustal formatted alignment Limitations: does not record the + consensus. Potential bug - records 60 chars length alignment where + Clustal would have recorded 50 chars. +

    +

    +
    Parameters:
    outStream -
    alignment - +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +readClustalFile

    +
    +public static Alignment readClustalFile(java.io.File file)
+                                 throws UnknownFileFormatException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    UnknownFileFormatException +
    java.io.IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/FastaSequence.html new file mode 100644 index 0000000..07a1dcf --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/FastaSequence.html @@ -0,0 +1,448 @@ + + + + + + +FastaSequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class FastaSequence

    +
    +java.lang.Object
+  extended by compbio.data.sequence.FastaSequence
+
    +
    +
    +
    @Immutable
+public class FastaSequence
    extends java.lang.Object
    + + +

    +A FASTA formatted sequence. Please note that this class does not make any + assumptions as to what sequence it store e.g. it could be nucleotide, protein + or even gapped alignment sequence! The only guarantee it makes is that the + sequence does not contain white space characters e.g. spaces, new lines etc +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    FastaSequence(java.lang.String id, + java.lang.String sequence) + +
    +          Upon construction the any whitespace characters are removed from the + sequence
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static intcountMatchesInSequence(java.lang.String theString, + java.lang.String theRegExp) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetFormatedSequence(int width) + +
    +          Format sequence per width letter in one string.
    + java.lang.StringgetFormattedFasta() + +
    +           
    + java.lang.StringgetId() + +
    +          Gets the value of id
    + intgetLength() + +
    +           
    + java.lang.StringgetOnelineFasta() + +
    +           
    + java.lang.StringgetSequence() + +
    +          Gets the value of sequence
    + java.lang.StringtoString() + +
    +          Same as oneLineFasta
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +FastaSequence

    +
    +public FastaSequence(java.lang.String id,
+                     java.lang.String sequence)
    +
    +
    Upon construction the any whitespace characters are removed from the + sequence +

    +

    +
    Parameters:
    id -
    sequence -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getId

    +
    +public java.lang.String getId()
    +
    +
    Gets the value of id +

    +

    + +
    Returns:
    the value of id
    +
    +
    +
    + +

    +getSequence

    +
    +public java.lang.String getSequence()
    +
    +
    Gets the value of sequence +

    +

    + +
    Returns:
    the value of sequence
    +
    +
    +
    + +

    +countMatchesInSequence

    +
    +public static int countMatchesInSequence(java.lang.String theString,
+                                         java.lang.String theRegExp)
    +
    +
    +
    +
    +
    +
    + +

    +getFormattedFasta

    +
    +public java.lang.String getFormattedFasta()
    +
    +
    +
    +
    +
    +
    + +

    +getOnelineFasta

    +
    +public java.lang.String getOnelineFasta()
    +
    +
    + +
    Returns:
    one line name, next line sequence, no matter what the sequence + length is
    +
    +
    +
    + +

    +getFormatedSequence

    +
    +public java.lang.String getFormatedSequence(int width)
    +
    +
    Format sequence per width letter in one string. Without spaces. +

    +

    + +
    Returns:
    multiple line formated sequence, one line width letters length
    +
    +
    +
    + +

    +getLength

    +
    +public int getLength()
    +
    +
    + +
    Returns:
    sequence length
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    Same as oneLineFasta +

    +

    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/Program.html b/website/full_javadoc/compbio/data/sequence/Program.html new file mode 100644 index 0000000..4c68bca --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/Program.html @@ -0,0 +1,388 @@ + + + + + + +Program + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Enum Program

    +
    +java.lang.Object
+  extended by java.lang.Enum<Program>
+      extended by compbio.data.sequence.Program
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Program>
    +
    +
    +
    +
    public enum Program
    extends java.lang.Enum<Program>
    + + +

    +Programmes that can produce alignments +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    CLUSTAL + +
    +          ClustalW
    MAFFT + +
    +          Mafft
    MUSCLE + +
    +          Muscle
    Probcons + +
    +          Probcons
    Tcoffee + +
    +          Tcoffee
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ProgramvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Program[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +CLUSTAL

    +
    +public static final Program CLUSTAL
    +
    +
    ClustalW +

    +

    +
    +
    +
    + +

    +MAFFT

    +
    +public static final Program MAFFT
    +
    +
    Mafft +

    +

    +
    +
    +
    + +

    +MUSCLE

    +
    +public static final Program MUSCLE
    +
    +
    Muscle +

    +

    +
    +
    +
    + +

    +Tcoffee

    +
    +public static final Program Tcoffee
    +
    +
    Tcoffee +

    +

    +
    +
    +
    + +

    +Probcons

    +
    +public static final Program Probcons
    +
    +
    Probcons +

    +

    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Program[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (Program c : Program.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static Program valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html new file mode 100644 index 0000000..a7bdf1a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/SequenceUtil.html @@ -0,0 +1,624 @@ + + + + + + +SequenceUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class SequenceUtil

    +
    +java.lang.Object
+  extended by compbio.data.sequence.SequenceUtil
+
    +
    +
    +
    public final class SequenceUtil
    extends java.lang.Object
    + + +

    +Utility class for operations on sequences +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date September 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.util.regex.PatternAA + +
    +          Valid Amino acids
    +static java.util.regex.PatternAMBIGUOUS_AA + +
    +          Same as AA pattern but with two additional letters - XU
    +static java.util.regex.PatternAMBIGUOUS_NUCLEOTIDE + +
    +          Ambiguous nucleotide
    +static java.util.regex.PatternDIGIT + +
    +          A digit
    +static java.util.regex.PatternNON_AA + +
    +          inversion of AA pattern
    +static java.util.regex.PatternNON_NUCLEOTIDE + +
    +          Non nucleotide
    +static java.util.regex.PatternNONWORD + +
    +          Non word
    +static java.util.regex.PatternNUCLEOTIDE + +
    +          Nucleotides a, t, g, c, u
    +static java.util.regex.PatternWHITE_SPACE + +
    +          A whitespace character: [\t\n\x0B\f\r]
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringcleanSequence(java.lang.String sequence) + +
    +          Removes all whitespace chars in the sequence string
    +static java.lang.StringdeepCleanSequence(java.lang.String sequence) + +
    +          Removes all special characters and digits as well as whitespace chars + from the sequence
    +static booleanisAmbiguosProtein(java.lang.String sequence) + +
    +          Check whether the sequence confirms to amboguous protein sequence
    +static booleanisNonAmbNucleotideSequence(java.lang.String sequence) + +
    +          Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char
    +static booleanisNucleotideSequence(FastaSequence s) + +
    +           
    +static booleanisProteinSequence(java.lang.String sequence) + +
    +           
    +static java.util.List<FastaSequence>readFasta(java.io.InputStream inStream) + +
    +          Reads fasta sequences from inStream into the list of FastaSequence + objects
    +static voidwriteFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
    +          Writes FastaSequence in the file, each sequence will take one line only
    +static voidwriteFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
    +          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +WHITE_SPACE

    +
    +public static final java.util.regex.Pattern WHITE_SPACE
    +
    +
    A whitespace character: [\t\n\x0B\f\r] +

    +

    +
    +
    +
    + +

    +DIGIT

    +
    +public static final java.util.regex.Pattern DIGIT
    +
    +
    A digit +

    +

    +
    +
    +
    + +

    +NONWORD

    +
    +public static final java.util.regex.Pattern NONWORD
    +
    +
    Non word +

    +

    +
    +
    +
    + +

    +AA

    +
    +public static final java.util.regex.Pattern AA
    +
    +
    Valid Amino acids +

    +

    +
    +
    +
    + +

    +NON_AA

    +
    +public static final java.util.regex.Pattern NON_AA
    +
    +
    inversion of AA pattern +

    +

    +
    +
    +
    + +

    +AMBIGUOUS_AA

    +
    +public static final java.util.regex.Pattern AMBIGUOUS_AA
    +
    +
    Same as AA pattern but with two additional letters - XU +

    +

    +
    +
    +
    + +

    +NUCLEOTIDE

    +
    +public static final java.util.regex.Pattern NUCLEOTIDE
    +
    +
    Nucleotides a, t, g, c, u +

    +

    +
    +
    +
    + +

    +AMBIGUOUS_NUCLEOTIDE

    +
    +public static final java.util.regex.Pattern AMBIGUOUS_NUCLEOTIDE
    +
    +
    Ambiguous nucleotide +

    +

    +
    +
    +
    + +

    +NON_NUCLEOTIDE

    +
    +public static final java.util.regex.Pattern NON_NUCLEOTIDE
    +
    +
    Non nucleotide +

    +

    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +isNucleotideSequence

    +
    +public static boolean isNucleotideSequence(FastaSequence s)
    +
    +
    + +
    Returns:
    true is the sequence contains only letters a,c, t, g, u
    +
    +
    +
    + +

    +isNonAmbNucleotideSequence

    +
    +public static boolean isNonAmbNucleotideSequence(java.lang.String sequence)
    +
    +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +

    +

    +
    +
    +
    +
    + +

    +cleanSequence

    +
    +public static java.lang.String cleanSequence(java.lang.String sequence)
    +
    +
    Removes all whitespace chars in the sequence string +

    +

    +
    Parameters:
    sequence - +
    Returns:
    cleaned up sequence
    +
    +
    +
    + +

    +deepCleanSequence

    +
    +public static java.lang.String deepCleanSequence(java.lang.String sequence)
    +
    +
    Removes all special characters and digits as well as whitespace chars + from the sequence +

    +

    +
    Parameters:
    sequence - +
    Returns:
    cleaned up sequence
    +
    +
    +
    + +

    +isProteinSequence

    +
    +public static boolean isProteinSequence(java.lang.String sequence)
    +
    +
    +
    Parameters:
    sequence - +
    Returns:
    true is the sequence is a protein sequence, false overwise
    +
    +
    +
    + +

    +isAmbiguosProtein

    +
    +public static boolean isAmbiguosProtein(java.lang.String sequence)
    +
    +
    Check whether the sequence confirms to amboguous protein sequence +

    +

    +
    Parameters:
    sequence - +
    Returns:
    return true only if the sequence if ambiguous protein sequence + Return false otherwise. e.g. if the sequence is non-ambiguous + protein or DNA
    +
    +
    +
    + +

    +writeFasta

    +
    +public static void writeFasta(java.io.OutputStream outstream,
+                              java.util.List<FastaSequence> sequences,
+                              int width)
+                       throws java.io.IOException
    +
    +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +

    +

    +
    Parameters:
    outstream -
    sequences -
    width - - the maximum number of characters to write in one line +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +readFasta

    +
    +public static java.util.List<FastaSequence> readFasta(java.io.InputStream inStream)
+                                               throws java.io.IOException
    +
    +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +

    +

    +
    Parameters:
    inStream - from +
    Returns:
    list of FastaSequence objects +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +writeFasta

    +
    +public static void writeFasta(java.io.OutputStream os,
+                              java.util.List<FastaSequence> sequences)
+                       throws java.io.IOException
    +
    +
    Writes FastaSequence in the file, each sequence will take one line only +

    +

    +
    Parameters:
    os -
    sequences - +
    Throws: +
    java.io.IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html new file mode 100644 index 0000000..d45a4ea --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/UnknownFileFormatException.html @@ -0,0 +1,300 @@ + + + + + + +UnknownFileFormatException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.data.sequence +
    +Class UnknownFileFormatException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.data.sequence.UnknownFileFormatException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class UnknownFileFormatException
    extends java.lang.Exception
    + + +

    +

    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    UnknownFileFormatException() + +
    +           
    UnknownFileFormatException(java.io.File file, + java.lang.Throwable cause) + +
    +           
    UnknownFileFormatException(java.lang.String message) + +
    +           
    UnknownFileFormatException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    UnknownFileFormatException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException()
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.io.File file,
+                                  java.lang.Throwable cause)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.String message,
+                                  java.lang.Throwable cause)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.String message)
    +
    +
    +
    + +

    +UnknownFileFormatException

    +
    +public UnknownFileFormatException(java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html new file mode 100644 index 0000000..af197d7 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/Alignment.html @@ -0,0 +1,433 @@ + + + + + + +Uses of Class compbio.data.sequence.Alignment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.Alignment

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Alignment
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Alignment in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Alignment
    + AlignmentMsaWS.getResult(java.lang.String jobId) + +
    +          Return the result of the job.
    +  +

    + + + + + +
    +Uses of Alignment in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return Alignment
    + AlignmentGetResultResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type Alignment
    + voidGetResultResponse.setReturn(Alignment _return) + +
    +           
    +  +

    + + + + + +
    +Uses of Alignment in compbio.data.sequence
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that return Alignment
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) + +
    +           
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +  +

    + + + + + + + + + +
    Methods in compbio.data.sequence with parameters of type Alignment
    +static voidClustalAlignmentUtil.writeClustalAlignment(java.io.OutputStream outStream, + Alignment alignment) + +
    +          Write Clustal formatted alignment Limitations: does not record the + consensus.
    +  +

    + + + + + +
    +Uses of Alignment in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return Alignment
    +static AlignmentUtil.readClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +  +

    + + + + + +
    +Uses of Alignment in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Alignment
    + AlignmentTcoffee.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentClustalW.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentProbcons.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMuscle.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMafft.getResults(java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of Alignment in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return Alignment
    + AlignmentTcoffeeWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentProbconsWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMuscleWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMafftWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentClustalWS.getResult(java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html new file mode 100644 index 0000000..efa449b --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/AlignmentMetadata.html @@ -0,0 +1,196 @@ + + + + + + +Uses of Class compbio.data.sequence.AlignmentMetadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +
    +

    +Uses of Class
    compbio.data.sequence.AlignmentMetadata

    +
    + + + + + + + + + +
    +Packages that use AlignmentMetadata
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of AlignmentMetadata in compbio.data.sequence
    +  +

    + + + + + + + + + +
    Methods in compbio.data.sequence that return AlignmentMetadata
    + AlignmentMetadataAlignment.getMetadata() + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.data.sequence with parameters of type AlignmentMetadata
    Alignment(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html new file mode 100644 index 0000000..6a07291 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/ClustalAlignmentUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.ClustalAlignmentUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.ClustalAlignmentUtil

    +
    +No usage of compbio.data.sequence.ClustalAlignmentUtil +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html new file mode 100644 index 0000000..cbc8cd7 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/FastaSequence.html @@ -0,0 +1,718 @@ + + + + + + +Uses of Class compbio.data.sequence.FastaSequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.data.sequence.FastaSequence

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use FastaSequence
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.engine  
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.pipeline._jpred  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.data.msa with type arguments of type FastaSequence
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return types with arguments of type FastaSequence
    + java.util.List<FastaSequence>PresetAlign.getFastaSequences() + +
    +           
    + java.util.List<FastaSequence>CustomAlign.getFastaSequences() + +
    +           
    + java.util.List<FastaSequence>Align.getFastaSequences() + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.data.msa.jaxws with type arguments of type FastaSequence
    + voidPresetAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidCustomAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    + voidAlign.setFastaSequences(java.util.List<FastaSequence> fastaSequences) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.data.sequence
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that return types with arguments of type FastaSequence
    + java.util.List<FastaSequence>Alignment.getSequences() + +
    +           
    +static java.util.List<FastaSequence>SequenceUtil.readFasta(java.io.InputStream inStream) + +
    +          Reads fasta sequences from inStream into the list of FastaSequence + objects
    +  +

    + + + + + + + + + +
    Methods in compbio.data.sequence with parameters of type FastaSequence
    +static booleanSequenceUtil.isNucleotideSequence(FastaSequence s) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.data.sequence with type arguments of type FastaSequence
    +static voidSequenceUtil.writeFasta(java.io.OutputStream os, + java.util.List<FastaSequence> sequences) + +
    +          Writes FastaSequence in the file, each sequence will take one line only
    +static voidSequenceUtil.writeFasta(java.io.OutputStream outstream, + java.util.List<FastaSequence> sequences, + int width) + +
    +          Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line
    +  +

    + + + + + + + + + + + +
    Constructor parameters in compbio.data.sequence with type arguments of type FastaSequence
    Alignment(java.util.List<FastaSequence> sequences, + AlignmentMetadata metadata) + +
    +           
    Alignment(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.engine with type arguments of type FastaSequence
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		LoadBalancer.getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type FastaSequence
    +static intLimit.getAvgSequenceLength(java.util.List<FastaSequence> data) + +
    +          Calculates an average sequence length of the dataset
    + booleanLimit.isExceeded(java.util.List<FastaSequence> data) + +
    +          Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.pipeline._jpred
    +  +

    + + + + + + + + +
    Constructor parameters in compbio.pipeline._jpred with type arguments of type FastaSequence
    Pairwise(java.util.List<FastaSequence> sequences) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.runner
    +  +

    + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type FastaSequence
    +static voidUtil.writeInput(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
    +           
    +  +

    + + + + + +
    +Uses of FastaSequence in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type FastaSequence
    + java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +static voidWSUtil.validateFastaInput(java.util.List<FastaSequence> sequences) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/Program.html b/website/full_javadoc/compbio/data/sequence/class-use/Program.html new file mode 100644 index 0000000..bfc36ba --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/Program.html @@ -0,0 +1,221 @@ + + + + + + +Uses of Class compbio.data.sequence.Program + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.data.sequence.Program

    +
    + + + + + + + + + +
    +Packages that use Program
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Program in compbio.data.sequence
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that return Program
    + ProgramAlignmentMetadata.getProgram() + +
    +           
    +static ProgramProgram.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Program[]Program.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + + + +
    Constructors in compbio.data.sequence with parameters of type Program
    Alignment(java.util.List<FastaSequence> sequences, + Program program, + char gapchar) + +
    +           
    AlignmentMetadata(Program program, + char gapchar) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html b/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html new file mode 100644 index 0000000..03ed214 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/SequenceUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.data.sequence.SequenceUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.data.sequence.SequenceUtil

    +
    +No usage of compbio.data.sequence.SequenceUtil +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html new file mode 100644 index 0000000..a24599c --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html @@ -0,0 +1,219 @@ + + + + + + +Uses of Class compbio.data.sequence.UnknownFileFormatException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.data.sequence.UnknownFileFormatException

    +
    + + + + + + + + + + + + + +
    +Packages that use UnknownFileFormatException
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    +  +

    + + + + + +
    +Uses of UnknownFileFormatException in compbio.data.sequence
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.sequence that throw UnknownFileFormatException
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.File file) + +
    +           
    +static AlignmentClustalAlignmentUtil.readClustalFile(java.io.InputStream instream) + +
    +          Read Clustal formatted alignment.
    +  +

    + + + + + +
    +Uses of UnknownFileFormatException in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that throw UnknownFileFormatException
    +static AlignmentUtil.readClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-frame.html b/website/full_javadoc/compbio/data/sequence/package-frame.html new file mode 100644 index 0000000..a4e673c --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-frame.html @@ -0,0 +1,62 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + +compbio.data.sequence + + + + +
    +Classes  + +
    +Alignment +
    +AlignmentMetadata +
    +ClustalAlignmentUtil +
    +FastaSequence +
    +SequenceUtil
    + + + + + + +
    +Enums  + +
    +Program
    + + + + + + +
    +Exceptions  + +
    +UnknownFileFormatException
    + + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html new file mode 100644 index 0000000..04cec6a --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-summary.html @@ -0,0 +1,223 @@ + + + + + + +compbio.data.sequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.data.sequence +

    +A data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    AlignmentMultiple sequence alignment.
    AlignmentMetadataAlignment metadata e.g.
    ClustalAlignmentUtilTools to read and write clustal formated files
    FastaSequenceA FASTA formatted sequence.
    SequenceUtilUtility class for operations on sequences
    +  + +

    + + + + + + + + + +
    +Enum Summary
    ProgramProgrammes that can produce alignments
    +  + +

    + + + + + + + + + +
    +Exception Summary
    UnknownFileFormatException 
    +  + +

    +

    +Package compbio.data.sequence Description +

    + +

    +A data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-tree.html b/website/full_javadoc/compbio/data/sequence/package-tree.html new file mode 100644 index 0000000..fab7633 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-tree.html @@ -0,0 +1,168 @@ + + + + + + +compbio.data.sequence Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
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    +
    +

    +Hierarchy For Package compbio.data.sequence +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/data/sequence/package-use.html b/website/full_javadoc/compbio/data/sequence/package-use.html new file mode 100644 index 0000000..2aeb78d --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/package-use.html @@ -0,0 +1,378 @@ + + + + + + +Uses of Package compbio.data.sequence + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.data.sequence

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.data.sequence
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.engine  
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.pipeline._jpred  
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.data.msa
    Alignment + +
    +          Multiple sequence alignment.
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.data.msa.jaxws
    Alignment + +
    +          Multiple sequence alignment.
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.data.sequence
    Alignment + +
    +          Multiple sequence alignment.
    AlignmentMetadata + +
    +          Alignment metadata e.g.
    FastaSequence + +
    +          A FASTA formatted sequence.
    Program + +
    +          Programmes that can produce alignments
    UnknownFileFormatException + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.engine
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.metadata
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.pipeline._jpred
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.runner
    Alignment + +
    +          Multiple sequence alignment.
    FastaSequence + +
    +          A FASTA formatted sequence.
    UnknownFileFormatException + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.runner.msa
    Alignment + +
    +          Multiple sequence alignment.
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.data.sequence used by compbio.ws.server
    Alignment + +
    +          Multiple sequence alignment.
    FastaSequence + +
    +          A FASTA formatted sequence.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/AsyncExecutor.html b/website/full_javadoc/compbio/engine/AsyncExecutor.html new file mode 100644 index 0000000..b5f9af4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/AsyncExecutor.html @@ -0,0 +1,344 @@ + + + + + + +AsyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Interface AsyncExecutor

    +
    +
    All Known Implementing Classes:
    AsyncJobRunner, AsyncLocalRunner
    +
    +
    +
    +
    public interface AsyncExecutor
    + + +

    +An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface. + Implementation agnostic. Executables can be run either locally to the JVM or on the cluster. +

    + +

    +

    +
    Author:
    +
    pvtroshin + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Query the status of the job
    + ConfiguredExecutable<?>getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +submitJob

    +
    +java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
    +
    +
    Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue. +

    +

    + +
    Returns:
    unique job identifier +
    Throws: +
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    +
    +
    +
    + +

    +getResults

    +
    +ConfiguredExecutable<?> getResults(java.lang.String jobId)
+                                   throws ResultNotAvailableException
    +
    +
    Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation. +

    +

    +
    Parameters:
    jobId - job identifier obtained at the job submission +
    Returns:
    ConfiguredExecutable object from which result can be obtained +
    Throws: +
    ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    +
    + +

    +cleanup

    +
    +boolean cleanup(java.lang.String jobId)
    +
    +
    Remove all files and a job directory for a jobid. +

    +

    +
    Parameters:
    jobId - +
    Returns:
    true if job directory was successfully removed, false otherwise.
    +
    +
    +
    + +

    +cancelJob

    +
    +boolean cancelJob(java.lang.String jobId)
    +
    +
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. +

    +

    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Query the status of the job +

    +

    +
    Parameters:
    String - jobId - unique job identifier +
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/Cleaner.html b/website/full_javadoc/compbio/engine/Cleaner.html new file mode 100644 index 0000000..f5a3e89 --- /dev/null +++ b/website/full_javadoc/compbio/engine/Cleaner.html @@ -0,0 +1,278 @@ + + + + + + +Cleaner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class Cleaner

    +
    +java.lang.Object
+  extended by compbio.engine.Cleaner
+
    +
    +
    +
    public class Cleaner
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Cleaner() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleandeleteAllFiles(java.lang.String directory) + +
    +           
    +static booleandeleteFiles(ConfiguredExecutable<?> exec) + +
    +          This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty)
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Cleaner

    +
    +public Cleaner()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +deleteFiles

    +
    +public static boolean deleteFiles(ConfiguredExecutable<?> exec)
    +
    +
    This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty) +

    +

    +
    Parameters:
    workDirectory -
    files - +
    Returns:
    +
    +
    +
    + +

    +deleteAllFiles

    +
    +public static boolean deleteAllFiles(java.lang.String directory)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/ClusterJobId.html b/website/full_javadoc/compbio/engine/ClusterJobId.html new file mode 100644 index 0000000..cedced1 --- /dev/null +++ b/website/full_javadoc/compbio/engine/ClusterJobId.html @@ -0,0 +1,297 @@ + + + + + + +ClusterJobId + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class ClusterJobId

    +
    +java.lang.Object
+  extended by compbio.engine.ClusterJobId
+
    +
    +
    +
    @Immutable
+public class ClusterJobId
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ClusterJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetJobId() + +
    +           
    + inthashCode() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ClusterJobId

    +
    +public ClusterJobId(java.lang.String jobId)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/Configurator.html b/website/full_javadoc/compbio/engine/Configurator.html new file mode 100644 index 0000000..61bbed4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/Configurator.html @@ -0,0 +1,538 @@ + + + + + + +Configurator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class Configurator

    +
    +java.lang.Object
+  extended by compbio.engine.Configurator
+
    +
    +
    +
    public class Configurator
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringCLUSTER_WORK_DIRECTORY + +
    +           
    +static booleanIS_CLUSTER_ENGINE_ENABLED + +
    +           
    +static booleanIS_LOCAL_ENGINE_ENABLED + +
    +           
    +static java.lang.StringLOCAL_WORK_DIRECTORY + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Configurator() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		configureExecutable(Executable<T> executable) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		configureExecutable(Executable<T> executable, + Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		configureExecutable(Executable<T> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static AsyncExecutorgetAsyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static AsyncExecutorgetAsyncEngine(java.lang.String taskId) + +
    +           
    +static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorgetSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringgetWorkDirectory(java.lang.String taskId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +IS_LOCAL_ENGINE_ENABLED

    +
    +public static final boolean IS_LOCAL_ENGINE_ENABLED
    +
    +
    +
    +
    +
    + +

    +IS_CLUSTER_ENGINE_ENABLED

    +
    +public static final boolean IS_CLUSTER_ENGINE_ENABLED
    +
    +
    +
    +
    +
    + +

    +LOCAL_WORK_DIRECTORY

    +
    +public static final java.lang.String LOCAL_WORK_DIRECTORY
    +
    +
    +
    +
    +
    + +

    +CLUSTER_WORK_DIRECTORY

    +
    +public static final java.lang.String CLUSTER_WORK_DIRECTORY
    +
    +
    +
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Configurator

    +
    +public Configurator()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +configureExecutable

    +
    +public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable)
+                                                   throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +configureExecutable

    +
    +public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
+                                                              java.util.List<FastaSequence> dataSet)
+                                                   throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +configureExecutable

    +
    +public static <T> ConfiguredExecutable<T> configureExecutable(Executable<T> executable,
+                                                              Executable.ExecProvider provider)
+                                                   throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getAsyncEngine

    +
    +public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable,
+                                           Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getSyncEngine

    +
    +public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable,
+                                         Executable.ExecProvider provider)
+                                  throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getAsyncEngine

    +
    +public static AsyncExecutor getAsyncEngine(ConfiguredExecutable<?> executable)
    +
    +
    +
    +
    +
    +
    + +

    +getAsyncEngine

    +
    +public static AsyncExecutor getAsyncEngine(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +getSyncEngine

    +
    +public static SyncExecutor getSyncEngine(ConfiguredExecutable<?> executable)
+                                  throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public static java.lang.String getWorkDirectory(java.lang.String taskId)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/FilePuller.html b/website/full_javadoc/compbio/engine/FilePuller.html new file mode 100644 index 0000000..5a017ae --- /dev/null +++ b/website/full_javadoc/compbio/engine/FilePuller.html @@ -0,0 +1,551 @@ + + + + + + +FilePuller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class FilePuller

    +
    +java.lang.Object
+  extended by compbio.engine.FilePuller
+
    +
    +
    All Implemented Interfaces:
    java.lang.Comparable<java.util.concurrent.Delayed>, java.util.concurrent.Delayed
    +
    +
    +
    +
    public class FilePuller
    extends java.lang.Object
    implements java.util.concurrent.Delayed
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intcompareTo(java.util.concurrent.Delayed o) + +
    +           
    + voiddisconnect() + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + longgetDelay(java.util.concurrent.TimeUnit unit) + +
    +           
    + java.lang.StringgetFile() + +
    +           
    + bytegetProgress() + +
    +           
    + inthashCode() + +
    +           
    + booleanhasMoreData() + +
    +           
    + voidinitPull() + +
    +           
    + booleanisFileCreated() + +
    +           
    +static FilePullernewFilePuller(java.lang.String file, + int chunkSize) + +
    +           
    +static FilePullernewProgressPuller(java.lang.String file) + +
    +          Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more.
    + ChunkHolderpull(long position) + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidwaitForFile(long maxWaitSeconds) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +newFilePuller

    +
    +public static FilePuller newFilePuller(java.lang.String file,
+                                       int chunkSize)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +newProgressPuller

    +
    +public static FilePuller newProgressPuller(java.lang.String file)
    +
    +
    Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more. Intended to be used in conjunction with a tool + which output progress as a percent value from 0 to 100. In any cases + progress could not be more than the largest byte value 255. +

    +

    +
    +
    +
    +
    Parameters:
    file - +
    Returns:
    +
    +
    +
    + +

    +pull

    +
    +public ChunkHolder pull(long position)
+                 throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +initPull

    +
    +public void initPull()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getFile

    +
    +public java.lang.String getFile()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +isFileCreated

    +
    +public boolean isFileCreated()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +waitForFile

    +
    +public void waitForFile(long maxWaitSeconds)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +hasMoreData

    +
    +public boolean hasMoreData()
+                    throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +compareTo

    +
    +public int compareTo(java.util.concurrent.Delayed o)
    +
    +
    +
    Specified by:
    compareTo in interface java.lang.Comparable<java.util.concurrent.Delayed>
    +
    +
    +
    +
    +
    +
    + +

    +getDelay

    +
    +public long getDelay(java.util.concurrent.TimeUnit unit)
    +
    +
    +
    Specified by:
    getDelay in interface java.util.concurrent.Delayed
    +
    +
    +
    +
    +
    +
    + +

    +disconnect

    +
    +public void disconnect()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public byte getProgress()
+                 throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/Job.html b/website/full_javadoc/compbio/engine/Job.html new file mode 100644 index 0000000..dc4790d --- /dev/null +++ b/website/full_javadoc/compbio/engine/Job.html @@ -0,0 +1,403 @@ + + + + + + +Job + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class Job

    +
    +java.lang.Object
+  extended by compbio.engine.Job
+
    +
    +
    +
    @Immutable
+public final class Job
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Job(java.lang.String taskId, + java.lang.String jobId, + ConfiguredExecutable<?> cexecutable) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    +static JobgetByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobgetByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    + ConfiguredExecutable<?>getConfExecutable() + +
    +           
    + ClusterJobIdgetJobId() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Job

    +
    +public Job(java.lang.String taskId,
+           java.lang.String jobId,
+           ConfiguredExecutable<?> cexecutable)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public ClusterJobId getJobId()
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +public java.lang.String getTaskId()
    +
    +
    +
    +
    +
    +
    + +

    +getConfExecutable

    +
    +public ConfiguredExecutable<?> getConfExecutable()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getByTaskId

    +
    +public static Job getByTaskId(java.lang.String taskId,
+                              java.util.List<Job> jobs)
    +
    +
    +
    +
    +
    +
    + +

    +getByJobId

    +
    +public static Job getByJobId(java.lang.String jobId,
+                             java.util.List<Job> jobs)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/LoadBalancer.html b/website/full_javadoc/compbio/engine/LoadBalancer.html new file mode 100644 index 0000000..eb3b1d9 --- /dev/null +++ b/website/full_javadoc/compbio/engine/LoadBalancer.html @@ -0,0 +1,247 @@ + + + + + + +LoadBalancer + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class LoadBalancer

    +
    +java.lang.Object
+  extended by compbio.engine.LoadBalancer
+
    +
    +
    +
    public class LoadBalancer
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + +
    +Method Summary
    +static Executable.ExecProvidergetEngine(Executable<?> executable) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getEngine

    +
    +public static Executable.ExecProvider getEngine(Executable<?> executable)
    +
    +
    +
    +
    +
    +
    + +

    +getEngine

    +
    +public static <T,V> Executable.ExecProvider getEngine(Executable<V> executable,
+                                                      java.util.List<FastaSequence> dataSet)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/ProgressGetter.html b/website/full_javadoc/compbio/engine/ProgressGetter.html new file mode 100644 index 0000000..93c4cd3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/ProgressGetter.html @@ -0,0 +1,273 @@ + + + + + + +ProgressGetter + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class ProgressGetter

    +
    +java.lang.Object
+  extended by compbio.engine.ProgressGetter
+
    +
    +
    +
    public class ProgressGetter
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ProgressGetter() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static bytegetProgress(java.lang.String progressFile) + +
    +           
    +static ChunkHolderpull(java.lang.String file, + long position) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ProgressGetter

    +
    +public ProgressGetter()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +pull

    +
    +public static final ChunkHolder pull(java.lang.String file,
+                                     long position)
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public static final byte getProgress(java.lang.String progressFile)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/PulledFileCache.html b/website/full_javadoc/compbio/engine/PulledFileCache.html new file mode 100644 index 0000000..0d11dcf --- /dev/null +++ b/website/full_javadoc/compbio/engine/PulledFileCache.html @@ -0,0 +1,275 @@ + + + + + + +PulledFileCache + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class PulledFileCache

    +
    +java.lang.Object
+  extended by compbio.engine.PulledFileCache
+
    +
    +
    +
    public final class PulledFileCache
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PulledFileCache() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static FilePullerget(java.lang.String fileName) + +
    +           
    +static booleanput(FilePuller fpuller) + +
    +          This method allows duplicates to be added.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PulledFileCache

    +
    +public PulledFileCache()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +get

    +
    +public static FilePuller get(java.lang.String fileName)
    +
    +
    +
    +
    +
    +
    + +

    +put

    +
    +public static boolean put(FilePuller fpuller)
    +
    +
    This method allows duplicates to be added. This is a responsibility of + the called to ensure this will not happen! +

    +

    +
    Parameters:
    fpuller - +
    Returns:
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/SubmissionManager.html b/website/full_javadoc/compbio/engine/SubmissionManager.html new file mode 100644 index 0000000..9a83cd7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/SubmissionManager.html @@ -0,0 +1,286 @@ + + + + + + +SubmissionManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Class SubmissionManager

    +
    +java.lang.Object
+  extended by compbio.engine.SubmissionManager
+
    +
    +
    +
    public class SubmissionManager
    extends java.lang.Object
    + + +

    +Submit jobs for execution +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static voidaddTask(ConfiguredExecutable<?> executable, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static java.util.concurrent.Future<ConfiguredExecutable<?>>getTask(java.lang.String taskId) + +
    +           
    +static voidremoveTask(ConfiguredExecutable<?> executable) + +
    +           
    +static voidremoveTask(java.lang.String key) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +addTask

    +
    +public static void addTask(ConfiguredExecutable<?> executable,
+                           java.util.concurrent.Future<ConfiguredExecutable<?>> future)
    +
    +
    +
    +
    +
    +
    + +

    +getTask

    +
    +public static java.util.concurrent.Future<ConfiguredExecutable<?>> getTask(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +removeTask

    +
    +public static void removeTask(ConfiguredExecutable<?> executable)
    +
    +
    +
    +
    +
    +
    + +

    +removeTask

    +
    +public static void removeTask(java.lang.String key)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/SyncExecutor.html b/website/full_javadoc/compbio/engine/SyncExecutor.html new file mode 100644 index 0000000..ac2be71 --- /dev/null +++ b/website/full_javadoc/compbio/engine/SyncExecutor.html @@ -0,0 +1,337 @@ + + + + + + +SyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine +
    +Interface SyncExecutor

    +
    +
    All Known Implementing Classes:
    JobRunner, LocalRunner
    +
    +
    +
    +
    public interface SyncExecutor
    + + +

    +Synchronous executor, is an engine to run the Executable synchronously. +

    + +

    +

    +
    Author:
    +
    pvtroshin + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob() + +
    +          Stops running job.
    + booleancleanup() + +
    +          Clean up after the job
    + voidexecuteJob() + +
    +          Execute the job
    + JobStatusgetJobStatus() + +
    +          Query the status of the job by its id.
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>waitForResult() + +
    +          Call to this method block for as long as it is required for an executable to finish its job.
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +executeJob

    +
    +void executeJob()
+                throws JobSubmissionException
    +
    +
    Execute the job +

    +

    + +
    Throws: +
    JobSubmissionException - if submission fails
    +
    +
    +
    + +

    +cleanup

    +
    +boolean cleanup()
    +
    +
    Clean up after the job +

    +

    + +
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    +
    +
    +
    + +

    +waitForResult

    +
    +ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
    +
    +
    Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe +

    +

    + +
    Returns:
    object from wich the result can be obtained +
    Throws: +
    JobExecutionException
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +java.lang.String getWorkDirectory()
    +
    +
    + +
    Returns:
    working directory if the task
    +
    +
    +
    + +

    +cancelJob

    +
    +boolean cancelJob()
    +
    +
    Stops running job. + Clean up is not performed. +

    +

    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +JobStatus getJobStatus()
    +
    +
    Query the status of the job by its id. +

    +

    + +
    Returns:
    - JobStatus
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html new file mode 100644 index 0000000..b28efa7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/AsyncExecutor.html @@ -0,0 +1,285 @@ + + + + + + +Uses of Interface compbio.engine.AsyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Interface
    compbio.engine.AsyncExecutor

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use AsyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of AsyncExecutor in compbio.engine
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine that return AsyncExecutor
    +static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static AsyncExecutorConfigurator.getAsyncEngine(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of AsyncExecutor in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.cluster.drmaa that implement AsyncExecutor
    + classAsyncJobRunner + +
    +          Single cluster job runner class
    +  +

    + + + + + +
    +Uses of AsyncExecutor in compbio.engine.local
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.local that implement AsyncExecutor
    + classAsyncLocalRunner + +
    +           
    +  +

    + + + + + +
    +Uses of AsyncExecutor in compbio.ws.server
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.server that return AsyncExecutor
    +static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Cleaner.html b/website/full_javadoc/compbio/engine/class-use/Cleaner.html new file mode 100644 index 0000000..2817a0e --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Cleaner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.Cleaner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.Cleaner

    +
    +No usage of compbio.engine.Cleaner +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html b/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html new file mode 100644 index 0000000..b2ba6dc --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/ClusterJobId.html @@ -0,0 +1,227 @@ + + + + + + +Uses of Class compbio.engine.ClusterJobId + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.ClusterJobId

    +
    + + + + + + + + + + + + + +
    +Packages that use ClusterJobId
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +Uses of ClusterJobId in compbio.engine
    +  +

    + + + + + + + + + +
    Methods in compbio.engine that return ClusterJobId
    + ClusterJobIdJob.getJobId() + +
    +           
    +  +

    + + + + + +
    +Uses of ClusterJobId in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that return ClusterJobId
    +static ClusterJobIdClusterSession.getClusterJobId(java.lang.String taskId) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa with parameters of type ClusterJobId
    + intClusterSession.getJobStatus(ClusterJobId jobId) + +
    +          Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Configurator.html b/website/full_javadoc/compbio/engine/class-use/Configurator.html new file mode 100644 index 0000000..40b9770 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Configurator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.Configurator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.Configurator

    +
    +No usage of compbio.engine.Configurator +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/FilePuller.html b/website/full_javadoc/compbio/engine/class-use/FilePuller.html new file mode 100644 index 0000000..c27be52 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/FilePuller.html @@ -0,0 +1,214 @@ + + + + + + +Uses of Class compbio.engine.FilePuller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.FilePuller

    +
    + + + + + + + + + +
    +Packages that use FilePuller
    compbio.engine  
    +  +

    + + + + + +
    +Uses of FilePuller in compbio.engine
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine that return FilePuller
    +static FilePullerPulledFileCache.get(java.lang.String fileName) + +
    +           
    +static FilePullerFilePuller.newFilePuller(java.lang.String file, + int chunkSize) + +
    +           
    +static FilePullerFilePuller.newProgressPuller(java.lang.String file) + +
    +          Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more.
    +  +

    + + + + + + + + + +
    Methods in compbio.engine with parameters of type FilePuller
    +static booleanPulledFileCache.put(FilePuller fpuller) + +
    +          This method allows duplicates to be added.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/Job.html b/website/full_javadoc/compbio/engine/class-use/Job.html new file mode 100644 index 0000000..def898e --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/Job.html @@ -0,0 +1,216 @@ + + + + + + +Uses of Class compbio.engine.Job + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.Job

    +
    + + + + + + + + + +
    +Packages that use Job
    compbio.engine  
    +  +

    + + + + + +
    +Uses of Job in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return Job
    +static JobJob.getByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobJob.getByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.engine with type arguments of type Job
    +static JobJob.getByJobId(java.lang.String jobId, + java.util.List<Job> jobs) + +
    +           
    +static JobJob.getByTaskId(java.lang.String taskId, + java.util.List<Job> jobs) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html b/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html new file mode 100644 index 0000000..233f48a --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/LoadBalancer.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.LoadBalancer + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.LoadBalancer

    +
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    +

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    +Uses of Class
    compbio.engine.ProgressGetter

    +
    +No usage of compbio.engine.ProgressGetter +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html b/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html new file mode 100644 index 0000000..2454b33 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/PulledFileCache.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.PulledFileCache + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.PulledFileCache

    +
    +No usage of compbio.engine.PulledFileCache +

    +

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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html b/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html new file mode 100644 index 0000000..557e5c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/SubmissionManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.SubmissionManager + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.SubmissionManager

    +
    +No usage of compbio.engine.SubmissionManager +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html b/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html new file mode 100644 index 0000000..5bb0963 --- /dev/null +++ b/website/full_javadoc/compbio/engine/class-use/SyncExecutor.html @@ -0,0 +1,248 @@ + + + + + + +Uses of Interface compbio.engine.SyncExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.SyncExecutor

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use SyncExecutor
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +Uses of SyncExecutor in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return SyncExecutor
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of SyncExecutor in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.cluster.drmaa that implement SyncExecutor
    + classJobRunner + +
    +          Single cluster job runner class
    +  +

    + + + + + +
    +Uses of SyncExecutor in compbio.engine.local
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.local that implement SyncExecutor
    + classLocalRunner + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html new file mode 100644 index 0000000..3eb5b72 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ClusterNativeSpecExecutable.html @@ -0,0 +1,243 @@ + + + + + + +ClusterNativeSpecExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Interface ClusterNativeSpecExecutable<T>

    +
    +
    All Superinterfaces:
    Executable<T>
    +
    +
    +
    All Known Implementing Classes:
    Tcoffee
    +
    +
    +
    +
    public interface ClusterNativeSpecExecutable<T>
    extends Executable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetNativeSpecs() + +
    +           
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getNativeSpecs

    +
    +java.lang.String getNativeSpecs()
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/CommandBuilder.html new file mode 100644 index 0000000..a717442 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/CommandBuilder.html @@ -0,0 +1,582 @@ + + + + + + +CommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class CommandBuilder<T>

    +
    +java.lang.Object
+  extended by compbio.engine.client.CommandBuilder<T>
+
    +
    +
    +
    public class CommandBuilder<T>
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    CommandBuilder(java.lang.String nameValueSeparator) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidaddParams(java.util.List<java.lang.String> params) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.util.List<java.lang.String>getCommands() + +
    +           
    + java.lang.StringgetCommandString() + +
    +           
    + java.lang.StringgetParamValue(java.lang.String paramName) + +
    +           
    + inthashCode() + +
    +           
    + booleanhasParam(java.lang.String paramName) + +
    +           
    +static + + + + +
    +<T> CommandBuilder<T>
    +    		newCommandBuilder(java.util.List<? extends Option<T>> arguments, + java.lang.String nameValueSeparator) + +
    +          This produces the same result as getCommands method.
    + booleanremoveParam(java.lang.String paramName) + +
    +           
    + booleansetFirst(java.lang.String param) + +
    +           
    + booleansetLast(java.lang.String paramName) + +
    +           
    + booleansetLast(java.lang.String paramName, + java.lang.String paramValue) + +
    +           
    + booleansetParam(java.lang.String param) + +
    +           
    + booleansetParam(java.lang.String paramName, + java.lang.String paramValue) + +
    +           
    + voidsetParams(java.util.List<java.lang.String> params) + +
    +           
    + intsize() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +CommandBuilder

    +
    +public CommandBuilder(java.lang.String nameValueSeparator)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +addParams

    +
    +public void addParams(java.util.List<java.lang.String> params)
    +
    +
    +
    +
    +
    +
    + +

    +setParams

    +
    +public void setParams(java.util.List<java.lang.String> params)
    +
    +
    +
    +
    +
    +
    + +

    +hasParam

    +
    +public boolean hasParam(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setFirst

    +
    +public boolean setFirst(java.lang.String param)
    +
    +
    +
    +
    +
    +
    + +

    +setParam

    +
    +public boolean setParam(java.lang.String param)
    +
    +
    +
    +
    +
    +
    + +

    +setLast

    +
    +public boolean setLast(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setLast

    +
    +public boolean setLast(java.lang.String paramName,
+                       java.lang.String paramValue)
    +
    +
    +
    +
    +
    +
    + +

    +getParamValue

    +
    +public java.lang.String getParamValue(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +removeParam

    +
    +public boolean removeParam(java.lang.String paramName)
    +
    +
    +
    +
    +
    +
    + +

    +setParam

    +
    +public boolean setParam(java.lang.String paramName,
+                        java.lang.String paramValue)
    +
    +
    +
    +
    +
    +
    + +

    +getCommands

    +
    +public java.util.List<java.lang.String> getCommands()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandString

    +
    +public java.lang.String getCommandString()
    +
    +
    +
    +
    +
    +
    + +

    +newCommandBuilder

    +
    +public static <T> CommandBuilder<T> newCommandBuilder(java.util.List<? extends Option<T>> arguments,
+                                                      java.lang.String nameValueSeparator)
    +
    +
    This produces the same result as getCommands method. The only difference + is that it accepts a List of Options as an input +

    +

    +
    Parameters:
    arguments - +
    Returns:
    +
    +
    +
    + +

    +size

    +
    +public int size()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/ConfExecutable.html new file mode 100644 index 0000000..a6ea5cc --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ConfExecutable.html @@ -0,0 +1,1000 @@ + + + + + + +ConfExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class ConfExecutable<T>

    +
    +java.lang.Object
+  extended by compbio.engine.client.ConfExecutable<T>
+
    +
    +
    All Implemented Interfaces:
    ConfiguredExecutable<T>, Executable<T>, PipedExecutable<T>
    +
    +
    +
    +
    public class ConfExecutable<T>
    extends java.lang.Object
    implements ConfiguredExecutable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringCLUSTER_TASK_ID_PREFIX + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ConfExecutable(Executable<T> executable, + java.lang.String taskDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Executable<T>addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getEnvironment() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + Executable.ExecProvidergetExecProvider() + +
    +           
    + Executable<T>getExecutable() + +
    +           
    + java.lang.StringgetInput() + +
    +          Not all input paths are relative! Input path could be absolute!
    + Limit<T>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<T>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + RunConfigurationgetRunConfiguration() + +
    +           
    +static + + + + +
    +<V> LimitsManager<V>
    +    		getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) + +
    +          This method should be executed once and result of its execution reused.
    +static + + + + +
    +<V> RunnerConfig<V>
    +    		getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +static + + + + +
    +<V> PresetManager<V>
    +    		getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    + Executable.ExecProvidergetSupportedRuntimes() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(RunConfiguration rconf) + +
    +           
    +static ConfiguredExecutable<?>newConfExecutable(RunConfiguration rconf) + +
    +           
    + booleansaveRunConfiguration() + +
    +           
    + voidsetExecProvider(Executable.ExecProvider provider) + +
    +           
    + voidsetWorkDirectory(java.lang.String workDirectory) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +CLUSTER_TASK_ID_PREFIX

    +
    +public static final java.lang.String CLUSTER_TASK_ID_PREFIX
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ConfExecutable

    +
    +public ConfExecutable(Executable<T> executable,
+                      java.lang.String taskDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getExecProvider

    +
    +public Executable.ExecProvider getExecProvider()
    +
    +
    +
    Specified by:
    getExecProvider in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +setExecProvider

    +
    +public void setExecProvider(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
+                            throws UnsupportedRuntimeException
    +
    +
    +
    Specified by:
    getCommand in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    UnsupportedRuntimeException
    +
    +
    +
    + +

    +getSupportedRuntimes

    +
    +public Executable.ExecProvider getSupportedRuntimes()
    +
    +
    +
    Specified by:
    getSupportedRuntimes in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<T> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<T> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +public java.lang.String getTaskId()
    +
    +
    +
    Specified by:
    getTaskId in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +setWorkDirectory

    +
    +public void setWorkDirectory(java.lang.String workDirectory)
    +
    +
    +
    Specified by:
    setWorkDirectory in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory()
    +
    +
    +
    Specified by:
    getWorkDirectory in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Executable<T> addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Description copied from interface: Executable
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Specified by:
    addParameters in interface Executable<T>
    +
    +
    + +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    Specified by:
    getCreatedFiles in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    Not all input paths are relative! Input path could be absolute! +

    +

    +
    Specified by:
    getInput in interface Executable<T>
    +
    +
    +
    See Also:
    compbio.engine.client.Executable#getInputFiles()
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<T> getParameters()
    +
    +
    +
    Specified by:
    getParameters in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getExecutable

    +
    +public Executable<T> getExecutable()
    +
    +
    +
    Specified by:
    getExecutable in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults()
+             throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<T>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public static <V> RunnerConfig<V> getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz)
+                                        throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunnerPresets

    +
    +public static <V> PresetManager<V> getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz)
+                                         throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunnerLimits

    +
    +public static <V> LimitsManager<V> getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz)
+                                        throws java.io.IOException
    +
    +
    This method should be executed once and result of its execution reused. + If not used carefully it could slow down the system! +

    +

    +
    +
    +
    +
    Type Parameters:
    V -
    Parameters:
    clazz - +
    Returns:
    +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getEnvironment

    +
    +public java.util.Map<java.lang.String,java.lang.String> getEnvironment()
    +
    +
    +
    Specified by:
    getEnvironment in interface ConfiguredExecutable<T>
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public ConfiguredExecutable<?> loadRunConfiguration(RunConfiguration rconf)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +newConfExecutable

    +
    +public static ConfiguredExecutable<?> newConfExecutable(RunConfiguration rconf)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +saveRunConfiguration

    +
    +public boolean saveRunConfiguration()
+                             throws java.io.IOException
    +
    +
    +
    Specified by:
    saveRunConfiguration in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getRunConfiguration

    +
    +public RunConfiguration getRunConfiguration()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
+                                             throws java.io.IOException
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface ConfiguredExecutable<T>
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html new file mode 100644 index 0000000..1a59a09 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/ConfiguredExecutable.html @@ -0,0 +1,504 @@ + + + + + + +ConfiguredExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Interface ConfiguredExecutable<T>

    +
    +
    All Superinterfaces:
    Executable<T>, PipedExecutable<T>
    +
    +
    +
    All Known Implementing Classes:
    ConfExecutable
    +
    +
    +
    +
    public interface ConfiguredExecutable<T>
    extends Executable<T>, PipedExecutable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getEnvironment() + +
    +           
    + Executable.ExecProvidergetExecProvider() + +
    +           
    + Executable<T>getExecutable() + +
    +           
    + CommandBuilder<T>getParameters() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults() + +
    +           
    + Executable.ExecProvidergetSupportedRuntimes() + +
    +           
    + java.lang.StringgetTaskId() + +
    +           
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>loadRunConfiguration(java.io.InputStream input) + +
    +           
    + booleansaveRunConfiguration() + +
    +           
    + voidsetWorkDirectory(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getEnvironment

    +
    +java.util.Map<java.lang.String,java.lang.String> getEnvironment()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getTaskId

    +
    +java.lang.String getTaskId()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +java.lang.String getCommand(Executable.ExecProvider provider)
+                            throws JobSubmissionException
    +
    +
    +
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    +
    + +

    +getSupportedRuntimes

    +
    +Executable.ExecProvider getSupportedRuntimes()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +java.lang.String getWorkDirectory()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setWorkDirectory

    +
    +void setWorkDirectory(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +<V> V getResults()
+             throws ResultNotAvailableException
    +
    +
    +
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getExecutable

    +
    +Executable<T> getExecutable()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +CommandBuilder<T> getParameters()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +saveRunConfiguration

    +
    +boolean saveRunConfiguration()
+                             throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +ConfiguredExecutable<?> loadRunConfiguration(java.io.InputStream input)
+                                             throws java.io.IOException
    +
    +
    +
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +getExecProvider

    +
    +Executable.ExecProvider getExecProvider()
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html new file mode 100644 index 0000000..096638b --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/EnvVariableProcessor.html @@ -0,0 +1,294 @@ + + + + + + +EnvVariableProcessor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class EnvVariableProcessor

    +
    +java.lang.Object
+  extended by compbio.engine.client.EnvVariableProcessor
+
    +
    +
    +
    public class EnvVariableProcessor
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringPATH + +
    +          Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable
    +  + + + + + + + + + + +
    +Constructor Summary
    EnvVariableProcessor() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static java.util.Map<java.lang.String,java.lang.String>getEnvVariables(java.lang.String property, + java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +PATH

    +
    +public static final java.lang.String PATH
    +
    +
    Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable +

    +

    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +EnvVariableProcessor

    +
    +public EnvVariableProcessor()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getEnvVariables

    +
    +public static java.util.Map<java.lang.String,java.lang.String> getEnvVariables(java.lang.String property,
+                                                                               java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html new file mode 100644 index 0000000..085b7fc --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Executable.ExecProvider.html @@ -0,0 +1,341 @@ + + + + + + +Executable.ExecProvider + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Enum Executable.ExecProvider

    +
    +java.lang.Object
+  extended by java.lang.Enum<Executable.ExecProvider>
+      extended by compbio.engine.client.Executable.ExecProvider
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Executable.ExecProvider>
    +
    +
    +
    Enclosing interface:
    Executable<T>
    +
    +
    +
    +
    public static enum Executable.ExecProvider
    extends java.lang.Enum<Executable.ExecProvider>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    Any + +
    +           
    Cluster + +
    +           
    Local + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static Executable.ExecProvidervalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Executable.ExecProvider[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +Local

    +
    +public static final Executable.ExecProvider Local
    +
    +
    +
    +
    +
    + +

    +Cluster

    +
    +public static final Executable.ExecProvider Cluster
    +
    +
    +
    +
    +
    + +

    +Any

    +
    +public static final Executable.ExecProvider Any
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Executable.ExecProvider[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (Executable.ExecProvider c : Executable.ExecProvider.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static Executable.ExecProvider valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/Executable.html b/website/full_javadoc/compbio/engine/client/Executable.html new file mode 100644 index 0000000..9f7254f --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Executable.html @@ -0,0 +1,423 @@ + + + + + + +Executable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Interface Executable<T>

    +
    +
    Type Parameters:
    T -
    +
    +
    All Known Subinterfaces:
    ClusterNativeSpecExecutable<T>, ConfiguredExecutable<T>, PipedExecutable<T>
    +
    +
    +
    All Known Implementing Classes:
    _SkeletalCommandBuilder, BlastAll, ClustalW, ConfExecutable, Disembl, Mafft, Mcl, Muscle, NetNglyc, OB, Probcons, PsiBlast, PSIBlast, Ronn, RPSBlast, SkeletalExecutable, Tcoffee
    +
    +
    +
    +
    public interface Executable<T>
    + + +

    +Interface to a native executable. +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classExecutable.ExecProvider + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Executable<T>addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + Limit<T>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<T>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +addParameters

    +
    +Executable<T> addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Parameters:
    parameters - +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +java.lang.String getInput()
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +java.lang.String getOutput()
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +java.lang.String getError()
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +<V> V getResults(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +Limit<T> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +LimitsManager<T> getLimits()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/PathValidator.html b/website/full_javadoc/compbio/engine/client/PathValidator.html new file mode 100644 index 0000000..d83660e --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/PathValidator.html @@ -0,0 +1,362 @@ + + + + + + +PathValidator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class PathValidator

    +
    +java.lang.Object
+  extended by compbio.engine.client.PathValidator
+
    +
    +
    +
    public final class PathValidator
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PathValidator() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleanisAbsolutePath(java.lang.String path) + +
    +          Whether a certain path is absolute or not is operation system dependent!
    +static booleanisValidDirectory(java.lang.String directory) + +
    +           
    +static booleanisValidExecutable(java.lang.String command) + +
    +           
    +static voidvalidateDirectory(java.lang.String workDirectory) + +
    +           
    +static voidvalidateExecutable(java.lang.String command) + +
    +           
    +static voidvalidatePathNames(java.util.List<java.lang.String> filenames, + java.lang.String type) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PathValidator

    +
    +public PathValidator()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +isValidExecutable

    +
    +public static boolean isValidExecutable(java.lang.String command)
    +
    +
    +
    +
    +
    +
    + +

    +validateExecutable

    +
    +public static void validateExecutable(java.lang.String command)
+                               throws java.lang.IllegalArgumentException
    +
    +
    + +
    Throws: +
    java.lang.IllegalArgumentException
    +
    +
    +
    + +

    +isValidDirectory

    +
    +public static boolean isValidDirectory(java.lang.String directory)
    +
    +
    +
    +
    +
    +
    + +

    +validatePathNames

    +
    +public static void validatePathNames(java.util.List<java.lang.String> filenames,
+                                     java.lang.String type)
+                              throws java.lang.IllegalArgumentException
    +
    +
    +
    Parameters:
    filenames -
    type - - merely a string to be added to error message to explain what + type of files are lacking +
    Throws: +
    java.lang.IllegalArgumentException
    +
    +
    +
    + +

    +isAbsolutePath

    +
    +public static boolean isAbsolutePath(java.lang.String path)
    +
    +
    Whether a certain path is absolute or not is operation system dependent! +

    +

    +
    Parameters:
    path - +
    Returns:
    +
    +
    +
    + +

    +validateDirectory

    +
    +public static void validateDirectory(java.lang.String workDirectory)
+                              throws java.lang.IllegalArgumentException
    +
    +
    + +
    Throws: +
    java.lang.IllegalArgumentException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/PipedExecutable.html new file mode 100644 index 0000000..e3e7f54 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/PipedExecutable.html @@ -0,0 +1,228 @@ + + + + + + +PipedExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Interface PipedExecutable<T>

    +
    +
    Type Parameters:
    T -
    +
    +
    All Superinterfaces:
    Executable<T>
    +
    +
    +
    All Known Subinterfaces:
    ConfiguredExecutable<T>
    +
    +
    +
    All Known Implementing Classes:
    ConfExecutable, Mafft, Probcons, Tcoffee
    +
    +
    +
    +
    public interface PipedExecutable<T>
    extends Executable<T>
    + + +

    +This is a marker interface to indicate that the output of the process must be + captured. It is in generally better for the process to manage its own + streams, but some executables are not capable of this thus require different + handling +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getCreatedFiles, getError, getInput, getLimit, getLimits, getOutput, getParameters, getResults, loadRunConfiguration
    +  +

    + +

    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/RunConfiguration.html new file mode 100644 index 0000000..56783a6 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/RunConfiguration.html @@ -0,0 +1,572 @@ + + + + + + +RunConfiguration + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class RunConfiguration

    +
    +java.lang.Object
+  extended by compbio.engine.client.RunConfiguration
+
    +
    +
    +
    public class RunConfiguration
    extends java.lang.Object
    + + +

    +Value class for persisting ConfExecutable instances +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringrconfigFile + +
    +           
    +  + + + + + + + + + + + + + +
    +Constructor Summary
    RunConfiguration() + +
    +           
    RunConfiguration(ConfExecutable<?> cexec) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<?>getParameters() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + inthashCode() + +
    +           
    +static RunConfigurationload(java.io.InputStream input) + +
    +           
    + voidsetError(java.lang.String error) + +
    +           
    + voidsetInput(java.lang.String input) + +
    +           
    + voidsetOutput(java.lang.String output) + +
    +           
    + voidsetParameters(CommandBuilder<?> parameters) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +static booleanwrite(RunConfiguration rconf) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +rconfigFile

    +
    +public static final java.lang.String rconfigFile
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +RunConfiguration

    +
    +public RunConfiguration()
    +
    +
    +
    + +

    +RunConfiguration

    +
    +public RunConfiguration(ConfExecutable<?> cexec)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +write

    +
    +public static boolean write(RunConfiguration rconf)
+                     throws java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +load

    +
    +public static RunConfiguration load(java.io.InputStream input)
+                             throws java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +setOutput

    +
    +public void setOutput(java.lang.String output)
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<?> getParameters()
    +
    +
    +
    +
    +
    +
    + +

    +setParameters

    +
    +public void setParameters(CommandBuilder<?> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    +
    +
    +
    + +

    +setError

    +
    +public void setError(java.lang.String error)
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public void setInput(java.lang.String input)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html new file mode 100644 index 0000000..bc14f0c --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/SkeletalExecutable.html @@ -0,0 +1,641 @@ + + + + + + +SkeletalExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class SkeletalExecutable<T>

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<T>
+
    +
    +
    All Implemented Interfaces:
    Executable<T>
    +
    +
    +
    Direct Known Subclasses:
    ClustalW, Mafft, Muscle, Probcons, PsiBlast, Tcoffee
    +
    +
    +
    +
    public abstract class SkeletalExecutable<T>
    extends java.lang.Object
    implements Executable<T>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + + + +
    +Constructor Summary
    SkeletalExecutable() + +
    +           
    SkeletalExecutable(java.lang.String parameterKeyValueDelimiter) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Executable<T>addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetClusterSettings() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<T>getParameters(Executable.ExecProvider provider) + +
    +           
    +abstract  java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + inthashCode() + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + SkeletalExecutable<T>setError(java.lang.String errFile) + +
    +           
    + SkeletalExecutable<T>setInput(java.lang.String inFile) + +
    +           
    + SkeletalExecutable<T>setOutput(java.lang.String outFile) + +
    +           
    + Executable<T>setParameter(java.lang.String parameter) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    getLimit, getLimits, getResults
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SkeletalExecutable

    +
    +public SkeletalExecutable()
    +
    +
    +
    + +

    +SkeletalExecutable

    +
    +public SkeletalExecutable(java.lang.String parameterKeyValueDelimiter)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setInput

    +
    +public SkeletalExecutable<T> setInput(java.lang.String inFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setOutput

    +
    +public SkeletalExecutable<T> setOutput(java.lang.String outFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setError

    +
    +public SkeletalExecutable<T> setError(java.lang.String errFile)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<T> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Executable<T> addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Description copied from interface: Executable
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Specified by:
    addParameters in interface Executable<T>
    +
    +
    + +
    Returns:
    this Executable
    +
    +
    +
    + +

    +setParameter

    +
    +public Executable<T> setParameter(java.lang.String parameter)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    This method cannot really tell whether the files has actually been + created or not. It must be overridden as required. +

    +

    +
    Specified by:
    getCreatedFiles in interface Executable<T>
    +
    +
    +
    See Also:
    Executable.getCreatedFiles()
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    Specified by:
    getInput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<T>
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getClusterSettings

    +
    +public java.lang.String getClusterSettings()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public abstract java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html new file mode 100644 index 0000000..5574f03 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/Util.html @@ -0,0 +1,505 @@ + + + + + + +Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.client +
    +Class Util

    +
    +java.lang.Object
+  extended by compbio.engine.client.Util
+
    +
    +
    +
    public final class Util
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Util() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringconvertToAbsolute(java.lang.String relativePath) + +
    +           
    +static java.lang.StringgetCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) + +
    +           
    +static java.lang.StringgetExecProperty(java.lang.String propertySpec, + java.lang.Class<?> clazz) + +
    +           
    +static java.lang.StringgetExecProperty(java.lang.String propertySpec, + Executable<?> exec) + +
    +           
    +static java.lang.StringgetFullPath(java.lang.String workDirectory, + java.lang.String fileName) + +
    +           
    +static Executable.ExecProvidergetSupportedRuntimes(java.lang.Class<?> clazz) + +
    +           
    +static booleanisMarked(java.lang.String workDirectory, + JobStatus marker) + +
    +           
    +static booleanisValidJobId(java.lang.String key) + +
    +           
    +static ConfiguredExecutable<?>loadExecutable(java.lang.String taskId) + +
    +           
    +static java.util.Map<java.lang.String,java.lang.String>mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified, + java.util.Map<java.lang.String,java.lang.String> variables) + +
    +           
    +static voidwriteFile(java.lang.String workDirectory, + java.lang.String fileAndEventName, + java.lang.String content, + boolean override) + +
    +           
    +static booleanwriteMarker(java.lang.String workDirectory, + JobStatus fileType) + +
    +           
    +static voidwriteStatFile(java.lang.String workDirectory, + java.lang.String fileAndEventName) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Util

    +
    +public Util()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +isValidJobId

    +
    +public static boolean isValidJobId(java.lang.String key)
    +
    +
    +
    +
    +
    +
    + +

    +writeStatFile

    +
    +public static void writeStatFile(java.lang.String workDirectory,
+                                 java.lang.String fileAndEventName)
    +
    +
    +
    +
    +
    +
    + +

    +writeFile

    +
    +public static void writeFile(java.lang.String workDirectory,
+                             java.lang.String fileAndEventName,
+                             java.lang.String content,
+                             boolean override)
    +
    +
    +
    +
    +
    +
    + +

    +writeMarker

    +
    +public static final boolean writeMarker(java.lang.String workDirectory,
+                                        JobStatus fileType)
    +
    +
    +
    +
    +
    +
    + +

    +isMarked

    +
    +public static boolean isMarked(java.lang.String workDirectory,
+                               JobStatus marker)
    +
    +
    +
    +
    +
    +
    + +

    +mergeEnvVariables

    +
    +public static java.util.Map<java.lang.String,java.lang.String> mergeEnvVariables(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,
+                                                                                 java.util.Map<java.lang.String,java.lang.String> variables)
    +
    +
    +
    +
    +
    +
    + +

    +convertToAbsolute

    +
    +public static java.lang.String convertToAbsolute(java.lang.String relativePath)
    +
    +
    +
    +
    +
    +
    + +

    +getExecProperty

    +
    +public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               Executable<?> exec)
    +
    +
    +
    +
    +
    +
    + +

    +getExecProperty

    +
    +public static java.lang.String getExecProperty(java.lang.String propertySpec,
+                                               java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getFullPath

    +
    +public static java.lang.String getFullPath(java.lang.String workDirectory,
+                                           java.lang.String fileName)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public static java.lang.String getCommand(Executable.ExecProvider provider,
+                                          java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getSupportedRuntimes

    +
    +public static Executable.ExecProvider getSupportedRuntimes(java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +loadExecutable

    +
    +public static ConfiguredExecutable<?> loadExecutable(java.lang.String taskId)
+                                              throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html new file mode 100644 index 0000000..d57b7bd --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ClusterNativeSpecExecutable.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Interface compbio.engine.client.ClusterNativeSpecExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Interface
    compbio.engine.client.ClusterNativeSpecExecutable

    +
    + + + + + + + + + +
    +Packages that use ClusterNativeSpecExecutable
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    +  +

    + + + + + +
    +Uses of ClusterNativeSpecExecutable in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Classes in compbio.runner.msa that implement ClusterNativeSpecExecutable
    + classTcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html new file mode 100644 index 0000000..663f217 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/CommandBuilder.html @@ -0,0 +1,339 @@ + + + + + + +Uses of Class compbio.engine.client.CommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.client.CommandBuilder

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use CommandBuilder
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    +  +

    + + + + + +
    +Uses of CommandBuilder in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return CommandBuilder
    + CommandBuilder<T>ConfiguredExecutable.getParameters() + +
    +           
    + CommandBuilder<T>ConfExecutable.getParameters() + +
    +           
    + CommandBuilder<?>RunConfiguration.getParameters() + +
    +           
    + CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> CommandBuilder<T>
    +    		CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, + java.lang.String nameValueSeparator) + +
    +          This produces the same result as getCommands method.
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type CommandBuilder
    + voidRunConfiguration.setParameters(CommandBuilder<?> parameters) + +
    +           
    +  +

    + + + + + +
    +Uses of CommandBuilder in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return CommandBuilder
    + CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of CommandBuilder in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return CommandBuilder
    + CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of CommandBuilder in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.msa that return CommandBuilder
    + CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html new file mode 100644 index 0000000..e5755d1 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ConfExecutable.html @@ -0,0 +1,178 @@ + + + + + + +Uses of Class compbio.engine.client.ConfExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.ConfExecutable

    +
    + + + + + + + + + +
    +Packages that use ConfExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    +  +

    + + + + + +
    +Uses of ConfExecutable in compbio.engine.client
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.client with parameters of type ConfExecutable
    RunConfiguration(ConfExecutable<?> cexec) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html new file mode 100644 index 0000000..85add53 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html @@ -0,0 +1,744 @@ + + + + + + +Uses of Interface compbio.engine.client.ConfiguredExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Interface
    compbio.engine.client.ConfiguredExecutable

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use ConfiguredExecutable
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.engine
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine that return ConfiguredExecutable
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    + ConfiguredExecutable<?>Job.getConfExecutable() + +
    +           
    + ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    + ConfiguredExecutable<?>SyncExecutor.waitForResult() + +
    +          Call to this method block for as long as it is required for an executable to finish its job.
    +  +

    + + + + + + + + + +
    Methods in compbio.engine that return types with arguments of type ConfiguredExecutable
    +static java.util.concurrent.Future<ConfiguredExecutable<?>>SubmissionManager.getTask(java.lang.String taskId) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine with parameters of type ConfiguredExecutable
    +static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static booleanCleaner.deleteFiles(ConfiguredExecutable<?> exec) + +
    +          This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty)
    +static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static voidSubmissionManager.removeTask(ConfiguredExecutable<?> executable) + +
    +           
    + java.lang.StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  +

    + + + + + + + + + +
    Method parameters in compbio.engine with type arguments of type ConfiguredExecutable
    +static voidSubmissionManager.addTask(ConfiguredExecutable<?> executable, + java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine with parameters of type ConfiguredExecutable
    Job(java.lang.String taskId, + java.lang.String jobId, + ConfiguredExecutable<?> cexecutable) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.engine.client
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.client that implement ConfiguredExecutable
    + classConfExecutable<T> + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return ConfiguredExecutable
    +static ConfiguredExecutable<?>Util.loadExecutable(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>ConfiguredExecutable.loadRunConfiguration(java.io.InputStream input) + +
    +           
    + ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(java.io.InputStream input) + +
    +           
    + ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) + +
    +           
    +static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that return ConfiguredExecutable
    + ConfiguredExecutable<?>ClusterSession.getResults(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) + +
    +           
    + ConfiguredExecutable<?>JobRunner.waitForResult() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
    +static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) + +
    +           
    + java.lang.StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.cluster.drmaa with parameters of type ConfiguredExecutable
    JobRunner(ConfiguredExecutable<?> confExec) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.engine.local
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.local that return ConfiguredExecutable
    + ConfiguredExecutable<?>ExecutableWrapper.call() + +
    +          It is vital that output and error streams are captured immediately for + this call() to succeed.
    +static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>LocalRunner.waitForResult() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.local with parameters of type ConfiguredExecutable
    +static booleanLocalEngineUtil.cleanup(ConfiguredExecutable<?> confExecutable) + +
    +           
    + java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.engine.local with type arguments of type ConfiguredExecutable
    +static booleanLocalEngineUtil.cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String workDirectory) + +
    +           
    +static JobStatusLocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    +  +

    + + + + + + + + + + + +
    Constructors in compbio.engine.local with parameters of type ConfiguredExecutable
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    LocalRunner(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type ConfiguredExecutable
    +static voidUtil.writeInput(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
    +           
    +  +

    + + + + + +
    +Uses of ConfiguredExecutable in compbio.ws.server
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type ConfiguredExecutable
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +static AsyncExecutorWSUtil.getEngine(ConfiguredExecutable<?> confClustal) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html b/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html new file mode 100644 index 0000000..8647d6e --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/EnvVariableProcessor.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.client.EnvVariableProcessor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.EnvVariableProcessor

    +
    +No usage of compbio.engine.client.EnvVariableProcessor +

    +

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    +Uses of Class
    compbio.engine.client.Executable.ExecProvider

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Executable.ExecProvider
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return Executable.ExecProvider
    +static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		LoadBalancer.getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine with parameters of type Executable.ExecProvider
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + Executable.ExecProvider provider) + +
    +           
    +static AsyncExecutorConfigurator.getAsyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return Executable.ExecProvider
    + Executable.ExecProviderConfiguredExecutable.getExecProvider() + +
    +           
    + Executable.ExecProviderConfExecutable.getExecProvider() + +
    +           
    + Executable.ExecProviderConfiguredExecutable.getSupportedRuntimes() + +
    +           
    + Executable.ExecProviderConfExecutable.getSupportedRuntimes() + +
    +           
    +static Executable.ExecProviderUtil.getSupportedRuntimes(java.lang.Class<?> clazz) + +
    +           
    +static Executable.ExecProviderExecutable.ExecProvider.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Executable.ExecProvider[]Executable.ExecProvider.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type Executable.ExecProvider
    + java.lang.StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringUtil.getCommand(Executable.ExecProvider provider, + java.lang.Class<?> clazz) + +
    +           
    + CommandBuilder<T>SkeletalExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>Executable.getParameters(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<T>ConfExecutable.getParameters(Executable.ExecProvider provider) + +
    +           
    + voidConfExecutable.setExecProvider(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type Executable.ExecProvider
    + CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner._impl with parameters of type Executable.ExecProvider
    + java.lang.StringMcl.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringBlastAll.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringRPSBlast.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringRonn.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringPSIBlast.getCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringDisembl.getCommand(Executable.ExecProvider provider) + +
    +           
    + CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable.ExecProvider in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.msa with parameters of type Executable.ExecProvider
    + CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/Executable.html b/website/full_javadoc/compbio/engine/client/class-use/Executable.html new file mode 100644 index 0000000..d3f24c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/Executable.html @@ -0,0 +1,892 @@ + + + + + + +Uses of Interface compbio.engine.client.Executable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    +

    +Uses of Interface
    compbio.engine.client.Executable

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Executable
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.confClasses commonly used by both engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +Uses of Executable in compbio.engine
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine with parameters of type Executable
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +static Executable.ExecProviderLoadBalancer.getEngine(Executable<?> executable) + +
    +           
    +static + + + + +
    +<T,V> Executable.ExecProvider
    +    		LoadBalancer.getEngine(Executable<V> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Subinterfaces of Executable in compbio.engine.client
    + interfaceClusterNativeSpecExecutable<T> + +
    +           
    + interfaceConfiguredExecutable<T> + +
    +           
    + interfacePipedExecutable<T> + +
    +          This is a marker interface to indicate that the output of the process must be + captured.
    +  +

    + + + + + + + + + + + + + +
    Classes in compbio.engine.client that implement Executable
    + classConfExecutable<T> + +
    +           
    + classSkeletalExecutable<T> + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return Executable
    + Executable<T>SkeletalExecutable.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + Executable<T>Executable.addParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + Executable<T>ConfExecutable.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + Executable<T>ConfiguredExecutable.getExecutable() + +
    +           
    + Executable<T>ConfExecutable.getExecutable() + +
    +           
    + Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<T>SkeletalExecutable.setParameter(java.lang.String parameter) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that return types with arguments of type Executable
    +abstract  java.lang.Class<? extends Executable<?>>SkeletalExecutable.getType() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type Executable
    +static java.lang.StringUtil.getExecProperty(java.lang.String propertySpec, + Executable<?> exec) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.engine.client with type arguments of type Executable
    +static + + + + +
    +<V> LimitsManager<V>
    +    		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) + +
    +          This method should be executed once and result of its execution reused.
    +static + + + + +
    +<V> RunnerConfig<V>
    +    		ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +static + + + + +
    +<V> PresetManager<V>
    +    		ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.client with parameters of type Executable
    ConfExecutable(Executable<T> executable, + java.lang.String taskDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.engine.conf
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.conf that return types with arguments of type Executable
    +static java.lang.Class<Executable<?>>DirectoryManager.getClass(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner
    +  +

    + + + + + + + + + +
    Classes in compbio.runner that implement Executable
    + class_SkeletalCommandBuilder + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return Executable
    + Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Executable
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +static + + + + +
    +<T> LimitsManager<T>
    +    		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +static + + + + +
    +<T> PresetManager<T>
    +    		Util.getPresets(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static + + + + +
    +<T> RunnerConfig<T>
    +    		Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +  +

    + + + + + + + + +
    Constructor parameters in compbio.runner with type arguments of type Executable
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Classes in compbio.runner._impl that implement Executable
    + classBlastAll + +
    +           
    + classDisembl + +
    +           
    + classMcl + +
    +           
    + classNetNglyc + +
    +           
    + classOB + +
    +          TODO this needs fixing! Executable does not work
    + classPSIBlast + +
    +           
    + classRonn + +
    +           
    + classRPSBlast + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Executable
    + Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Classes in compbio.runner.msa that implement Executable
    + classClustalW + +
    +           
    + classMafft + +
    +           
    + classMuscle + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Executable
    + java.lang.Class<? extends Executable<?>>Tcoffee.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>ClustalW.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Probcons.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Muscle.getType() + +
    +           
    + java.lang.Class<? extends Executable<?>>Mafft.getType() + +
    +           
    +  +

    + + + + + +
    +Uses of Executable in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Classes in compbio.runner.psiblast that implement Executable
    + classPsiBlast + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return types with arguments of type Executable
    + java.lang.Class<? extends Executable<?>>PsiBlast.getType() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html b/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html new file mode 100644 index 0000000..9d4b585 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/PathValidator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.client.PathValidator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    +
    +

    +Uses of Class
    compbio.engine.client.PathValidator

    +
    +No usage of compbio.engine.client.PathValidator +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html new file mode 100644 index 0000000..2cb2e67 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/PipedExecutable.html @@ -0,0 +1,241 @@ + + + + + + +Uses of Interface compbio.engine.client.PipedExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Interface
    compbio.engine.client.PipedExecutable

    +
    + + + + + + + + + + + + + +
    +Packages that use PipedExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    +  +

    + + + + + +
    +Uses of PipedExecutable in compbio.engine.client
    +  +

    + + + + + + + + + +
    Subinterfaces of PipedExecutable in compbio.engine.client
    + interfaceConfiguredExecutable<T> + +
    +           
    +  +

    + + + + + + + + + +
    Classes in compbio.engine.client that implement PipedExecutable
    + classConfExecutable<T> + +
    +           
    +  +

    + + + + + +
    +Uses of PipedExecutable in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Classes in compbio.runner.msa that implement PipedExecutable
    + classMafft + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html b/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html new file mode 100644 index 0000000..656c2a0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/RunConfiguration.html @@ -0,0 +1,294 @@ + + + + + + +Uses of Class compbio.engine.client.RunConfiguration + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.client.RunConfiguration

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use RunConfiguration
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of RunConfiguration in compbio.engine.client
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return RunConfiguration
    + RunConfigurationConfExecutable.getRunConfiguration() + +
    +           
    +static RunConfigurationRunConfiguration.load(java.io.InputStream input) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type RunConfiguration
    + Executable<?>SkeletalExecutable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + Executable<?>Executable.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + ConfiguredExecutable<?>ConfExecutable.loadRunConfiguration(RunConfiguration rconf) + +
    +           
    +static ConfiguredExecutable<?>ConfExecutable.newConfExecutable(RunConfiguration rconf) + +
    +           
    +static booleanRunConfiguration.write(RunConfiguration rconf) + +
    +           
    +  +

    + + + + + +
    +Uses of RunConfiguration in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type RunConfiguration
    + Executable<?>_SkeletalCommandBuilder.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    + + + + + +
    +Uses of RunConfiguration in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl with parameters of type RunConfiguration
    + Executable<?>NetNglyc.loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html b/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html new file mode 100644 index 0000000..30e7933 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html @@ -0,0 +1,286 @@ + + + + + + +Uses of Class compbio.engine.client.SkeletalExecutable + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.client.SkeletalExecutable

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use SkeletalExecutable
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return SkeletalExecutable
    + SkeletalExecutable<T>SkeletalExecutable.setError(java.lang.String errFile) + +
    +           
    + SkeletalExecutable<T>SkeletalExecutable.setInput(java.lang.String inFile) + +
    +           
    + SkeletalExecutable<T>SkeletalExecutable.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Subclasses of SkeletalExecutable in compbio.runner.msa
    + classClustalW + +
    +           
    + classMafft + +
    +           
    + classMuscle + +
    +           
    + classProbcons + +
    +           
    + classTcoffee + +
    +           
    +  +

    + + + + + +
    +Uses of SkeletalExecutable in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Subclasses of SkeletalExecutable in compbio.runner.psiblast
    + classPsiBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.client.Util

    +
    +No usage of compbio.engine.client.Util +

    +

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    +Interfaces  + +
    +ClusterNativeSpecExecutable +
    +ConfiguredExecutable +
    +Executable +
    +PipedExecutable
    + + + + + + +
    +Classes  + +
    +CommandBuilder +
    +ConfExecutable +
    +EnvVariableProcessor +
    +PathValidator +
    +RunConfiguration +
    +SkeletalExecutable +
    +Util
    + + + + + + +
    +Enums  + +
    +Executable.ExecProvider
    + + + + diff --git a/website/full_javadoc/compbio/engine/client/package-summary.html b/website/full_javadoc/compbio/engine/client/package-summary.html new file mode 100644 index 0000000..8ce82d7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-summary.html @@ -0,0 +1,242 @@ + + + + + + +compbio.engine.client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Package compbio.engine.client +

    +Classes and interfaces representing an input for engines. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Interface Summary
    ClusterNativeSpecExecutable<T> 
    ConfiguredExecutable<T> 
    Executable<T>Interface to a native executable.
    PipedExecutable<T>This is a marker interface to indicate that the output of the process must be + captured.
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    CommandBuilder<T> 
    ConfExecutable<T> 
    EnvVariableProcessor 
    PathValidator 
    RunConfigurationValue class for persisting ConfExecutable instances
    SkeletalExecutable<T> 
    Util 
    +  + +

    + + + + + + + + + +
    +Enum Summary
    Executable.ExecProvider 
    +  + +

    +

    +Package compbio.engine.client Description +

    + +

    +Classes and interfaces representing an input for engines. These classes are known to runners, + which form the next layer of the JABAWS hierarchy. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/package-tree.html b/website/full_javadoc/compbio/engine/client/package-tree.html new file mode 100644 index 0000000..ce4996a --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-tree.html @@ -0,0 +1,176 @@ + + + + + + +compbio.engine.client Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.engine.client +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/client/package-use.html b/website/full_javadoc/compbio/engine/client/package-use.html new file mode 100644 index 0000000..010d2bf --- /dev/null +++ b/website/full_javadoc/compbio/engine/client/package-use.html @@ -0,0 +1,470 @@ + + + + + + +Uses of Package compbio.engine.client + + + + + + + + + + + + +
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    +Uses of Package
    compbio.engine.client

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.engine.client
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.confClasses commonly used by both engines. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.engine
    ConfiguredExecutable + +
    +           
    Executable + +
    +          Interface to a native executable.
    Executable.ExecProvider + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.engine.client
    CommandBuilder + +
    +           
    ConfExecutable + +
    +           
    ConfiguredExecutable + +
    +           
    Executable + +
    +          Interface to a native executable.
    Executable.ExecProvider + +
    +           
    PipedExecutable + +
    +          This is a marker interface to indicate that the output of the process must be + captured.
    RunConfiguration + +
    +          Value class for persisting ConfExecutable instances
    SkeletalExecutable + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.engine.cluster.drmaa
    ConfiguredExecutable + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.engine.conf
    Executable + +
    +          Interface to a native executable.
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.engine.local
    ConfiguredExecutable + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.runner
    CommandBuilder + +
    +           
    Executable + +
    +          Interface to a native executable.
    Executable.ExecProvider + +
    +           
    RunConfiguration + +
    +          Value class for persisting ConfExecutable instances
    +  +

    + + + + + + + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.runner._impl
    CommandBuilder + +
    +           
    Executable + +
    +          Interface to a native executable.
    Executable.ExecProvider + +
    +           
    RunConfiguration + +
    +          Value class for persisting ConfExecutable instances
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.runner.msa
    ClusterNativeSpecExecutable + +
    +           
    CommandBuilder + +
    +           
    Executable + +
    +          Interface to a native executable.
    Executable.ExecProvider + +
    +           
    PipedExecutable + +
    +          This is a marker interface to indicate that the output of the process must be + captured.
    SkeletalExecutable + +
    +           
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.runner.psiblast
    Executable + +
    +          Interface to a native executable.
    SkeletalExecutable + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.client used by compbio.ws.server
    ConfiguredExecutable + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html new file mode 100644 index 0000000..779a787 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/AsyncJobRunner.html @@ -0,0 +1,412 @@ + + + + + + +AsyncJobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class AsyncJobRunner

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.AsyncJobRunner
+
    +
    +
    All Implemented Interfaces:
    AsyncExecutor
    +
    +
    +
    +
    public class AsyncJobRunner
    extends java.lang.Object
    implements AsyncExecutor
    + + +

    +Single cluster job runner class +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AsyncJobRunner() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    + ConfiguredExecutable<?>getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +AsyncJobRunner

    +
    +public AsyncJobRunner()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +submitJob

    +
    +public java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue. +

    +

    +
    Specified by:
    submitJob in interface AsyncExecutor
    +
    +
    + +
    Returns:
    unique job identifier +
    Throws: +
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. +

    +

    +
    Specified by:
    cancelJob in interface AsyncExecutor
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed. Cancelled jobs needs to be + tracked manually! +

    +

    +
    Specified by:
    getJobStatus in interface AsyncExecutor
    +
    +
    + +
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    +
    +
    +
    + +

    +cleanup

    +
    +public boolean cleanup(java.lang.String jobId)
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Remove all files and a job directory for a jobid. +

    +

    +
    Specified by:
    cleanup in interface AsyncExecutor
    +
    +
    + +
    Returns:
    true if job directory was successfully removed, false otherwise.
    +
    +
    +
    + +

    +getResults

    +
    +public ConfiguredExecutable<?> getResults(java.lang.String jobId)
+                                   throws ResultNotAvailableException
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation. +

    +

    +
    Specified by:
    getResults in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - job identifier obtained at the job submission +
    Returns:
    ConfiguredExecutable object from which result can be obtained +
    Throws: +
    ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html new file mode 100644 index 0000000..51b0e22 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterSession.html @@ -0,0 +1,471 @@ + + + + + + +ClusterSession + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class ClusterSession

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.ClusterSession
+
    +
    +
    +
    public final class ClusterSession
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringJOBID + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidclose() + +
    +           
    +static ClusterJobIdgetClusterJobId(java.lang.String taskId) + +
    +           
    + intgetJobStatus(ClusterJobId jobId) + +
    +          Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed.
    +static java.lang.StringgetJobStatus(int status) + +
    +          Deprecated. 
    + ConfiguredExecutable<?>getResults(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.SessiongetSession() + +
    +           
    +static StatisticManagergetStatistics(org.ggf.drmaa.JobInfo status) + +
    +           
    + voidremoveJob(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.JobInfowaitForJob(java.lang.String taskId) + +
    +           
    + org.ggf.drmaa.JobInfowaitForJob(java.lang.String jobId, + long waitingTime) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +JOBID

    +
    +public static final java.lang.String JOBID
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getSession

    +
    +public org.ggf.drmaa.Session getSession()
    +
    +
    +
    +
    +
    +
    + +

    +close

    +
    +public void close()
    +
    +
    +
    +
    +
    +
    + +

    +removeJob

    +
    +public void removeJob(java.lang.String taskId)
    +
    +
    +
    +
    +
    +
    + +

    +waitForJob

    +
    +public org.ggf.drmaa.JobInfo waitForJob(java.lang.String taskId)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException +
    java.io.IOException
    +
    +
    +
    + +

    +getClusterJobId

    +
    +public static ClusterJobId getClusterJobId(java.lang.String taskId)
+                                    throws java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    +
    + +

    +waitForJob

    +
    +public org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId,
+                                        long waitingTime)
+                                 throws org.ggf.drmaa.DrmaaException,
+                                        java.io.IOException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException +
    java.io.IOException
    +
    +
    +
    + +

    +getResults

    +
    +public ConfiguredExecutable<?> getResults(java.lang.String taskId)
+                                   throws org.ggf.drmaa.DrmaaException,
+                                          ResultNotAvailableException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getStatistics

    +
    +public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
+                                      throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getJobStatus

    +
    +public int getJobStatus(ClusterJobId jobId)
+                 throws org.ggf.drmaa.DrmaaException,
+                        org.ggf.drmaa.InvalidJobException
    +
    +
    Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed. +

    +

    + +
    Throws: +
    org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it + will throw this exception for all finished or cancelled jobs +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getJobStatus

    +
    +@Deprecated
+public static java.lang.String getJobStatus(int status)
+                                     throws org.ggf.drmaa.DrmaaException
    +
    +
    Deprecated.  +

    +

    Method for getting jobs status by quering the cluster, It returns status + in therms of a Sessions, not a JobStatus Should only be used for testing! +

    +

    +
    Parameters:
    status - +
    Returns:
    +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html new file mode 100644 index 0000000..ad68763 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/ClusterUtil.html @@ -0,0 +1,314 @@ + + + + + + +ClusterUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class ClusterUtil

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.ClusterUtil
+
    +
    +
    +
    public class ClusterUtil
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.text.NumberFormatCLUSTER_STAT_IN_SEC + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ClusterUtil() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleancancelJob(java.lang.String jobId, + ClusterSession csession) + +
    +           
    +static org.ggf.drmaa.JobInfowaitForResult(ClusterSession csession, + java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +CLUSTER_STAT_IN_SEC

    +
    +public static final java.text.NumberFormat CLUSTER_STAT_IN_SEC
    +
    +
    +
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ClusterUtil

    +
    +public ClusterUtil()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +cancelJob

    +
    +public static final boolean cancelJob(java.lang.String jobId,
+                                      ClusterSession csession)
    +
    +
    +
    +
    +
    +
    + +

    +waitForResult

    +
    +public static final org.ggf.drmaa.JobInfo waitForResult(ClusterSession csession,
+                                                        java.lang.String jobId)
+                                                 throws JobExecutionException
    +
    +
    + +
    Throws: +
    JobExecutionException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html new file mode 100644 index 0000000..da7c2e3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/JobRunner.html @@ -0,0 +1,487 @@ + + + + + + +JobRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class JobRunner

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.JobRunner
+
    +
    +
    All Implemented Interfaces:
    SyncExecutor
    +
    +
    +
    +
    public class JobRunner
    extends java.lang.Object
    implements SyncExecutor
    + + +

    +Single cluster job runner class +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    JobRunner(ConfiguredExecutable<?> confExec) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob() + +
    +          Stops running job.
    + booleancleanup() + +
    +          Clean up after the job
    + booleandeepClean() + +
    +           
    + voidexecuteJob() + +
    +          Execute the job
    +static JobRunnergetInstance(ConfiguredExecutable<?> executable) + +
    +           
    + org.ggf.drmaa.JobInfogetJobInfo() + +
    +          This method will block before the calculation has completed and then + return the object containing a job execution statistics
    + JobStatusgetJobStatus() + +
    +          Query the status of the job by its id.
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>waitForResult() + +
    +          Call to this method block for as long as it is required for an executable to finish its job.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobRunner

    +
    +public JobRunner(ConfiguredExecutable<?> confExec)
+          throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +deepClean

    +
    +public boolean deepClean()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +cleanup

    +
    +public boolean cleanup()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Clean up after the job +

    +

    +
    Specified by:
    cleanup in interface SyncExecutor
    +
    +
    + +
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Stops running job. + Clean up is not performed. +

    +

    +
    Specified by:
    cancelJob in interface SyncExecutor
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory()
    +
    +
    +
    Specified by:
    getWorkDirectory in interface SyncExecutor
    +
    +
    + +
    Returns:
    working directory if the task
    +
    +
    +
    + +

    +executeJob

    +
    +public void executeJob()
+                throws JobSubmissionException
    +
    +
    Description copied from interface: SyncExecutor
    +
    Execute the job +

    +

    +
    Specified by:
    executeJob in interface SyncExecutor
    +
    +
    + +
    Throws: +
    JobSubmissionException - if submission fails
    +
    +
    +
    + +

    +getJobInfo

    +
    +public org.ggf.drmaa.JobInfo getJobInfo()
+                                 throws JobExecutionException
    +
    +
    This method will block before the calculation has completed and then + return the object containing a job execution statistics +

    +

    +
    +
    +
    + +
    Returns:
    +
    Throws: +
    JobExecutionException
    +
    +
    +
    + +

    +waitForResult

    +
    +public ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
    +
    +
    Description copied from interface: SyncExecutor
    +
    Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe +

    +

    +
    Specified by:
    waitForResult in interface SyncExecutor
    +
    +
    + +
    Returns:
    object from wich the result can be obtained +
    Throws: +
    JobExecutionException
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Query the status of the job by its id. +

    +

    +
    Specified by:
    getJobStatus in interface SyncExecutor
    +
    +
    + +
    Returns:
    - JobStatus
    +
    +
    +
    + +

    +getInstance

    +
    +public static JobRunner getInstance(ConfiguredExecutable<?> executable)
+                             throws JobSubmissionException
    +
    +
    +
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html new file mode 100644 index 0000000..da1ad93 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/StatisticManager.html @@ -0,0 +1,759 @@ + + + + + + +StatisticManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class StatisticManager

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa.StatisticManager
+
    +
    +
    +
    public class StatisticManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    StatisticManager(org.ggf.drmaa.JobInfo status) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetAllStats() + +
    +           
    + java.lang.StringgetCalculationTime() + +
    +           
    + java.lang.StringgetCPUTimeStat() + +
    +           
    + java.lang.StringgetCPUUsageTime() + +
    +           
    + java.lang.StringgetDataTransfered() + +
    +           
    + java.lang.StringgetEndTime() + +
    +           
    + java.lang.StringgetExecutionStat() + +
    +           
    + java.lang.StringgetExitStatus() + +
    +           
    + java.lang.StringgetIOWait() + +
    +           
    + java.lang.StringgetJobId() + +
    +           
    + java.lang.StringgetJobPriority() + +
    +           
    + java.lang.StringgetMaxVMem() + +
    +           
    + java.lang.StringgetMemoryStat() + +
    +           
    + java.util.Map<java.lang.String,java.lang.String>getRawUsage() + +
    +           
    + java.lang.StringgetStartTime() + +
    +           
    + java.lang.StringgetSubmissionTime() + +
    +           
    + java.lang.StringgetTimeStat() + +
    +           
    + java.lang.StringgetUsedSysTime() + +
    +           
    + java.lang.StringgetUsedUserTime() + +
    +           
    + java.lang.StringgetVMem() + +
    +           
    + booleanhasDump() + +
    +           
    + booleanhasExited() + +
    +           
    + booleanhasSignaled() + +
    +           
    + java.lang.StringtermSignal() + +
    +           
    + java.lang.StringtoString() + +
    +           
    + booleanwasAborted() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +StatisticManager

    +
    +public StatisticManager(org.ggf.drmaa.JobInfo status)
+                 throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getJobId

    +
    +public java.lang.String getJobId()
+                          throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +hasExited

    +
    +public boolean hasExited()
+                  throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +hasSignaled

    +
    +public boolean hasSignaled()
+                    throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +hasDump

    +
    +public boolean hasDump()
+                throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +termSignal

    +
    +public java.lang.String termSignal()
+                            throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +wasAborted

    +
    +public boolean wasAborted()
+                   throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getSubmissionTime

    +
    +public java.lang.String getSubmissionTime()
    +
    +
    +
    +
    +
    +
    + +

    +getVMem

    +
    +public java.lang.String getVMem()
    +
    +
    +
    +
    +
    +
    + +

    +getMaxVMem

    +
    +public java.lang.String getMaxVMem()
    +
    +
    +
    +
    +
    +
    + +

    +getUsedSysTime

    +
    +public java.lang.String getUsedSysTime()
    +
    +
    +
    +
    +
    +
    + +

    +getUsedUserTime

    +
    +public java.lang.String getUsedUserTime()
    +
    +
    +
    +
    +
    +
    + +

    +getCalculationTime

    +
    +public java.lang.String getCalculationTime()
    +
    +
    +
    +
    +
    +
    + +

    +getEndTime

    +
    +public java.lang.String getEndTime()
    +
    +
    +
    +
    +
    +
    + +

    +getStartTime

    +
    +public java.lang.String getStartTime()
    +
    +
    +
    +
    +
    +
    + +

    +getIOWait

    +
    +public java.lang.String getIOWait()
    +
    +
    +
    +
    +
    +
    + +

    +getCPUUsageTime

    +
    +public java.lang.String getCPUUsageTime()
    +
    +
    +
    +
    +
    +
    + +

    +getDataTransfered

    +
    +public java.lang.String getDataTransfered()
    +
    +
    +
    +
    +
    +
    + +

    +getJobPriority

    +
    +public java.lang.String getJobPriority()
    +
    +
    +
    +
    +
    +
    + +

    +getExitStatus

    +
    +public java.lang.String getExitStatus()
    +
    +
    +
    +
    +
    +
    + +

    +getAllStats

    +
    +public java.lang.String getAllStats()
+                             throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getExecutionStat

    +
    +public java.lang.String getExecutionStat()
+                                  throws org.ggf.drmaa.DrmaaException
    +
    +
    + +
    Throws: +
    org.ggf.drmaa.DrmaaException
    +
    +
    +
    + +

    +getMemoryStat

    +
    +public java.lang.String getMemoryStat()
    +
    +
    +
    +
    +
    +
    + +

    +getCPUTimeStat

    +
    +public java.lang.String getCPUTimeStat()
    +
    +
    +
    +
    +
    +
    + +

    +getTimeStat

    +
    +public java.lang.String getTimeStat()
    +
    +
    +
    +
    +
    +
    + +

    +getRawUsage

    +
    +public java.util.Map<java.lang.String,java.lang.String> getRawUsage()
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html new file mode 100644 index 0000000..158c30c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/_DrmaaExample.html @@ -0,0 +1,255 @@ + + + + + + +_DrmaaExample + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class _DrmaaExample

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa._DrmaaExample
+
    +
    +
    +
    public class _DrmaaExample
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _DrmaaExample() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_DrmaaExample

    +
    +public _DrmaaExample()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.lang.Exception
    +
    +
    + +
    Throws: +
    java.lang.Exception
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html b/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html new file mode 100644 index 0000000..6aaaf54 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/_JobStatus.html @@ -0,0 +1,252 @@ + + + + + + +_JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.drmaa +
    +Class _JobStatus

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.drmaa._JobStatus
+
    +
    +
    +
    public class _JobStatus
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _JobStatus() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_JobStatus

    +
    +public _JobStatus()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html new file mode 100644 index 0000000..1c73aaf --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/AsyncJobRunner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.AsyncJobRunner + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.cluster.drmaa.AsyncJobRunner

    +
    +No usage of compbio.engine.cluster.drmaa.AsyncJobRunner +

    +

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    +Uses of Class
    compbio.engine.cluster.drmaa.ClusterSession

    +
    + + + + + + + + + +
    +Packages that use ClusterSession
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +Uses of ClusterSession in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa with parameters of type ClusterSession
    +static booleanClusterUtil.cancelJob(java.lang.String jobId, + ClusterSession csession) + +
    +           
    +static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, + java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    compbio.engine.cluster.drmaa.ClusterUtil

    +
    +No usage of compbio.engine.cluster.drmaa.ClusterUtil +

    +

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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html new file mode 100644 index 0000000..4f09e88 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/JobRunner.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.JobRunner + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.cluster.drmaa.JobRunner

    +
    + + + + + + + + + +
    +Packages that use JobRunner
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +Uses of JobRunner in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that return JobRunner
    +static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html new file mode 100644 index 0000000..fc796c4 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/class-use/StatisticManager.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.cluster.drmaa.StatisticManager + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.cluster.drmaa.StatisticManager

    +
    + + + + + + + + + +
    +Packages that use StatisticManager
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + +
    +Uses of StatisticManager in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that return StatisticManager
    +static StatisticManagerClusterSession.getStatistics(org.ggf.drmaa.JobInfo status) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.cluster.drmaa._DrmaaExample

    +
    +No usage of compbio.engine.cluster.drmaa._DrmaaExample +

    +

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    +Uses of Class
    compbio.engine.cluster.drmaa._JobStatus

    +
    +No usage of compbio.engine.cluster.drmaa._JobStatus +

    +

    + + + + + + + + + + + + + + + +
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    +Classes  + +
    +_DrmaaExample +
    +_JobStatus +
    +AsyncJobRunner +
    +ClusterSession +
    +ClusterUtil +
    +JobRunner +
    +StatisticManager
    + + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html new file mode 100644 index 0000000..a995ad5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/package-summary.html @@ -0,0 +1,203 @@ + + + + + + +compbio.engine.cluster.drmaa + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +

    +Package compbio.engine.cluster.drmaa +

    +An cluster engine classes responsible for execution of Executables on the clusters. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _DrmaaExample 
    _JobStatus 
    AsyncJobRunnerSingle cluster job runner class
    ClusterSession 
    ClusterUtil 
    JobRunnerSingle cluster job runner class
    StatisticManager 
    +  + +

    +

    +Package compbio.engine.cluster.drmaa Description +

    + +

    +An cluster engine classes responsible for execution of Executables on the clusters. + Implementation uses DRMAA library. + Classes in this package depend on the data model classes. + They form a second layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html b/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html new file mode 100644 index 0000000..e51bdff --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/drmaa/package-tree.html @@ -0,0 +1,155 @@ + + + + + + +compbio.engine.cluster.drmaa Class Hierarchy + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.engine.cluster.drmaa +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
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    +

    +Uses of Package
    compbio.engine.cluster.drmaa

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.cluster.drmaa
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.engine.cluster.drmaa used by compbio.engine.cluster.drmaa
    ClusterSession + +
    +           
    JobRunner + +
    +          Single cluster job runner class
    StatisticManager + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html new file mode 100644 index 0000000..613a3c0 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/_Queue.html @@ -0,0 +1,517 @@ + + + + + + +_Queue + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.dundee +
    +Enum _Queue

    +
    +java.lang.Object
+  extended by java.lang.Enum<_Queue>
+      extended by compbio.engine.cluster.dundee._Queue
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<_Queue>
    +
    +
    +
    +
    public enum _Queue
    extends java.lang.Enum<_Queue>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    BIGINT + +
    +           
    BIGMEM + +
    +           
    BIT64 + +
    +           
    DEVEL + +
    +          Order of the constraint reflect the priority of the queue
    PRIBIT64 + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetMemoryLimit() + +
    +          return max memory limit in Mb
    +static _QueuegetQueue(int maxMemory, + int timeLimitInHours) + +
    +           
    + _QueuegetQueue(java.lang.String queueName) + +
    +           
    +static _QueuegetQueueByMemoryRequirements(int maxMemory) + +
    +           
    + intgetTimeLimit() + +
    +          0 - unlimited
    + booleanhasTimeLimit() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +static _QueuevalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static _Queue[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +DEVEL

    +
    +public static final _Queue DEVEL
    +
    +
    Order of the constraint reflect the priority of the queue +

    +

    +
    +
    +
    + +

    +PRIBIT64

    +
    +public static final _Queue PRIBIT64
    +
    +
    +
    +
    +
    + +

    +BIT64

    +
    +public static final _Queue BIT64
    +
    +
    +
    +
    +
    + +

    +BIGINT

    +
    +public static final _Queue BIGINT
    +
    +
    +
    +
    +
    + +

    +BIGMEM

    +
    +public static final _Queue BIGMEM
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static _Queue[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (_Queue c : _Queue.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static _Queue valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Enum<_Queue>
    +
    +
    +
    +
    +
    +
    + +

    +getTimeLimit

    +
    +public int getTimeLimit()
    +
    +
    0 - unlimited +

    +

    + +
    Returns:
    max runtime in hours
    +
    +
    +
    + +

    +hasTimeLimit

    +
    +public boolean hasTimeLimit()
    +
    +
    + +
    Returns:
    true if the queue has time limit, false overwise
    +
    +
    +
    + +

    +getMemoryLimit

    +
    +public int getMemoryLimit()
    +
    +
    return max memory limit in Mb +

    +

    + +
    Returns:
    +
    +
    +
    + +

    +getQueueByMemoryRequirements

    +
    +public static _Queue getQueueByMemoryRequirements(int maxMemory)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public static _Queue getQueue(int maxMemory,
+                              int timeLimitInHours)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public _Queue getQueue(java.lang.String queueName)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html new file mode 100644 index 0000000..f951552 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/_QueueConstraints.html @@ -0,0 +1,281 @@ + + + + + + +_QueueConstraints + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.cluster.dundee +
    +Class _QueueConstraints

    +
    +java.lang.Object
+  extended by compbio.engine.cluster.dundee._QueueConstraints
+
    +
    +
    +
    public final class _QueueConstraints
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Field Summary
    +static intFIRST_MEMORY_LIMIT + +
    +           
    +static intLONG_TIME_LIMIT + +
    +           
    +static intMAX_MEMORY_LIMIT + +
    +           
    +static intSHORT_TIME_LIMIT + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +SHORT_TIME_LIMIT

    +
    +public static final int SHORT_TIME_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +LONG_TIME_LIMIT

    +
    +public static final int LONG_TIME_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +FIRST_MEMORY_LIMIT

    +
    +public static final int FIRST_MEMORY_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +MAX_MEMORY_LIMIT

    +
    +public static final int MAX_MEMORY_LIMIT
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html new file mode 100644 index 0000000..d5b990c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_Queue.html @@ -0,0 +1,243 @@ + + + + + + +Uses of Class compbio.engine.cluster.dundee._Queue + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.cluster.dundee._Queue

    +
    + + + + + + + + + + + + + +
    +Packages that use _Queue
    compbio.engine.cluster.dundee  
    compbio.runnerUtilities commonly used by all runners. 
    +  +

    + + + + + +
    +Uses of _Queue in compbio.engine.cluster.dundee
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.dundee that return _Queue
    +static _Queue_Queue.getQueue(int maxMemory, + int timeLimitInHours) + +
    +           
    + _Queue_Queue.getQueue(java.lang.String queueName) + +
    +           
    +static _Queue_Queue.getQueueByMemoryRequirements(int maxMemory) + +
    +           
    +static _Queue_Queue.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static _Queue[]_Queue.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + +
    +Uses of _Queue in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return _Queue
    + _Queue_NativeSpecHelper.getApproprieteQueue() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html new file mode 100644 index 0000000..233b459 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/class-use/_QueueConstraints.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.cluster.dundee._QueueConstraints + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.engine.cluster.dundee._QueueConstraints

    +
    +No usage of compbio.engine.cluster.dundee._QueueConstraints +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html new file mode 100644 index 0000000..80f27d5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-frame.html @@ -0,0 +1,43 @@ + + + + + + +compbio.engine.cluster.dundee + + + + + + + + + + + +compbio.engine.cluster.dundee + + + + +
    +Classes  + +
    +_QueueConstraints
    + + + + + + +
    +Enums  + +
    +_Queue
    + + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html new file mode 100644 index 0000000..5cbb529 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-summary.html @@ -0,0 +1,171 @@ + + + + + + +compbio.engine.cluster.dundee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.cluster.dundee +

    + + + + + + + + + +
    +Class Summary
    _QueueConstraints 
    +  + +

    + + + + + + + + + +
    +Enum Summary
    _Queue 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html new file mode 100644 index 0000000..189d945 --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-tree.html @@ -0,0 +1,163 @@ + + + + + + +compbio.engine.cluster.dundee Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Hierarchy For Package compbio.engine.cluster.dundee +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) +
          +
        • compbio.engine.cluster.dundee._Queue
        +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html b/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html new file mode 100644 index 0000000..998ba3c --- /dev/null +++ b/website/full_javadoc/compbio/engine/cluster/dundee/package-use.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Package compbio.engine.cluster.dundee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    + + + +
    +
    +

    +Uses of Package
    compbio.engine.cluster.dundee

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.engine.cluster.dundee
    compbio.engine.cluster.dundee  
    compbio.runnerUtilities commonly used by all runners. 
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.cluster.dundee used by compbio.engine.cluster.dundee
    _Queue + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.cluster.dundee used by compbio.runner
    _Queue + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html new file mode 100644 index 0000000..f4e425b --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/DirectoryManager.html @@ -0,0 +1,307 @@ + + + + + + +DirectoryManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.conf +
    +Class DirectoryManager

    +
    +java.lang.Object
+  extended by compbio.engine.conf.DirectoryManager
+
    +
    +
    +
    public class DirectoryManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringDELIM + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    DirectoryManager() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.Class<Executable<?>>getClass(java.lang.String taskId) + +
    +           
    +static java.lang.StringgetTaskDirectory(java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +DELIM

    +
    +public static final java.lang.String DELIM
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +DirectoryManager

    +
    +public DirectoryManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTaskDirectory

    +
    +public static java.lang.String getTaskDirectory(java.lang.Class<?> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getClass

    +
    +public static java.lang.Class<Executable<?>> getClass(java.lang.String taskId)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html new file mode 100644 index 0000000..d4816f8 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/PropertyHelperManager.html @@ -0,0 +1,332 @@ + + + + + + +PropertyHelperManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.conf +
    +Class PropertyHelperManager

    +
    +java.lang.Object
+  extended by compbio.engine.conf.PropertyHelperManager
+
    +
    +
    +
    public final class PropertyHelperManager
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringconfDir + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    PropertyHelperManager() + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringgetLocalPath() + +
    +          Method return the absolute path to the project root directory.
    +static compbio.util.PropertyHelpergetPropertyHelper() + +
    +          Ways to fix path problem: 1) find a path to WEB-INF directory based on + the path to a known class.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +confDir

    +
    +public static final java.lang.String confDir
    +
    +
    +
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +PropertyHelperManager

    +
    +public PropertyHelperManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPropertyHelper

    +
    +public static compbio.util.PropertyHelper getPropertyHelper()
    +
    +
    Ways to fix path problem: 1) find a path to WEB-INF directory based on + the path to a known class. Then prepend this absolute path to the rest of + paths pros: no input from user cons: relocation of the source may cause + problems 2) Require users to add configuration directories to the class + path and then load entries from it. pros: cons: Many paths needs to be + added. Put significant burden on the user. Hard to tell web appl server + to add these entries to its class path. 3) Ask for project source + directory explicitly in the configuration. pros cons: similar to 1, but + this initial configuration file must reside in well known location! Why + ask users what can be found automatically? 4) Have everything in the + location already in class path for tomcat. cons: only classes and + lib/*.jar are added, eclipse will remove non classses from classes dir. + + Try 1 - succeed. +

    +

    + +
    Returns:
    +
    +
    +
    + +

    +getLocalPath

    +
    +public static java.lang.String getLocalPath()
    +
    +
    Method return the absolute path to the project root directory. It assumes + the following structure of the project project root conf settings + binaries WEB-INF classes compbio engine conf If the structure changes it + must be reflected in this method +

    +

    + +
    Returns:
    +
    Throws: +
    javax.naming.ConfigurationException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html new file mode 100644 index 0000000..6457ed8 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/RunnerConfigMarshaller.html @@ -0,0 +1,507 @@ + + + + + + +RunnerConfigMarshaller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.conf +
    +Class RunnerConfigMarshaller<T>

    +
    +java.lang.Object
+  extended by compbio.engine.conf.RunnerConfigMarshaller<T>
+
    +
    +
    +
    public class RunnerConfigMarshaller<T>
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    RunnerConfigMarshaller(java.lang.Class<?> rootClass) + +
    +           
    RunnerConfigMarshaller(java.lang.Class<?> rootClass, + java.lang.Class<?>... classes) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static javax.xml.validation.SchemagetSchema(java.lang.String schemafile) + +
    +           
    +static javax.xml.validation.ValidatorgetValidator(javax.xml.validation.Schema schema) + +
    +           
    +static javax.xml.validation.ValidatorgetValidator(java.lang.String schemafile) + +
    +           
    + + + + + +
    +<V> V
    +    		read(java.io.InputStream instream, + java.lang.Class<V> resultElemType) + +
    +           
    + + + + + +
    +<V> V
    +    		read(java.io.InputStream instream, + java.lang.Class<V> resultElemType, + java.lang.Class<?>... classes) + +
    +           
    + + + + + +
    +<V> V
    +    		readAndValidate(java.io.InputStream document, + java.lang.Class<V> resultElemType) + +
    +           
    +static booleanvalidate(javax.xml.validation.Validator validator, + java.lang.String document) + +
    +           
    + voidwrite(java.lang.Object xmlRootElement, + java.io.OutputStream out) + +
    +           
    + voidwriteAndValidate(java.lang.Object xmlRootElement, + java.lang.String schemafile, + java.io.OutputStream out) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +RunnerConfigMarshaller

    +
    +public RunnerConfigMarshaller(java.lang.Class<?> rootClass)
+                       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    + +

    +RunnerConfigMarshaller

    +
    +public RunnerConfigMarshaller(java.lang.Class<?> rootClass,
+                              java.lang.Class<?>... classes)
+                       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +write

    +
    +public void write(java.lang.Object xmlRootElement,
+                  java.io.OutputStream out)
+           throws javax.xml.bind.JAXBException,
+                  java.io.IOException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException
    +
    +
    +
    + +

    +writeAndValidate

    +
    +public void writeAndValidate(java.lang.Object xmlRootElement,
+                             java.lang.String schemafile,
+                             java.io.OutputStream out)
+                      throws javax.xml.bind.JAXBException,
+                             java.io.IOException,
+                             org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getSchema

    +
    +public static javax.xml.validation.Schema getSchema(java.lang.String schemafile)
+                                             throws org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getValidator

    +
    +public static javax.xml.validation.Validator getValidator(java.lang.String schemafile)
+                                                   throws org.xml.sax.SAXException
    +
    +
    + +
    Returns:
    +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +getValidator

    +
    +public static javax.xml.validation.Validator getValidator(javax.xml.validation.Schema schema)
+                                                   throws org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +validate

    +
    +public static boolean validate(javax.xml.validation.Validator validator,
+                               java.lang.String document)
+                        throws java.io.IOException,
+                               org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +readAndValidate

    +
    +public <V> V readAndValidate(java.io.InputStream document,
+                             java.lang.Class<V> resultElemType)
+                  throws javax.xml.bind.JAXBException,
+                         java.io.IOException,
+                         org.xml.sax.SAXException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException +
    java.io.IOException +
    org.xml.sax.SAXException
    +
    +
    +
    + +

    +read

    +
    +public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType)
+       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    +
    + +

    +read

    +
    +public <V> V read(java.io.InputStream instream,
+                  java.lang.Class<V> resultElemType,
+                  java.lang.Class<?>... classes)
+       throws javax.xml.bind.JAXBException
    +
    +
    + +
    Throws: +
    javax.xml.bind.JAXBException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/_Key.html b/website/full_javadoc/compbio/engine/conf/_Key.html new file mode 100644 index 0000000..68d1965 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/_Key.html @@ -0,0 +1,354 @@ + + + + + + +_Key + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.conf +
    +Class _Key

    +
    +java.lang.Object
+  extended by compbio.engine.conf._Key
+
    +
    +
    +
    public final class _Key
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringDELIM + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    _Key(java.lang.Class<?> clazz) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + inthashCode() + +
    +           
    +static _Keyparse(java.lang.String key) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +DELIM

    +
    +public static final java.lang.String DELIM
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +_Key

    +
    +public _Key(java.lang.Class<?> clazz)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +parse

    +
    +public static _Key parse(java.lang.String key)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html new file mode 100644 index 0000000..8152d4c --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/DirectoryManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.DirectoryManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.conf.DirectoryManager

    +
    +No usage of compbio.engine.conf.DirectoryManager +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html b/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html new file mode 100644 index 0000000..e8d0067 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/PropertyHelperManager.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.PropertyHelperManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.conf.PropertyHelperManager

    +
    +No usage of compbio.engine.conf.PropertyHelperManager +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html b/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html new file mode 100644 index 0000000..deeac1c --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/RunnerConfigMarshaller.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.conf.RunnerConfigMarshaller + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
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    +

    +Uses of Class
    compbio.engine.conf.RunnerConfigMarshaller

    +
    +No usage of compbio.engine.conf.RunnerConfigMarshaller +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/class-use/_Key.html b/website/full_javadoc/compbio/engine/conf/class-use/_Key.html new file mode 100644 index 0000000..223d824 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/class-use/_Key.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.engine.conf._Key + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Class
    compbio.engine.conf._Key

    +
    + + + + + + + + + +
    +Packages that use _Key
    compbio.engine.confClasses commonly used by both engines. 
    +  +

    + + + + + +
    +Uses of _Key in compbio.engine.conf
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.conf that return _Key
    +static _Key_Key.parse(java.lang.String key) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-frame.html b/website/full_javadoc/compbio/engine/conf/package-frame.html new file mode 100644 index 0000000..29f4ef3 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.engine.conf + + + + + + + + + + + +compbio.engine.conf + + + + +
    +Classes  + +
    +_Key +
    +DirectoryManager +
    +PropertyHelperManager +
    +RunnerConfigMarshaller
    + + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-summary.html b/website/full_javadoc/compbio/engine/conf/package-summary.html new file mode 100644 index 0000000..7dc8a3b --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-summary.html @@ -0,0 +1,188 @@ + + + + + + +compbio.engine.conf + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.engine.conf +

    +Classes commonly used by both engines. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _Key 
    DirectoryManager 
    PropertyHelperManager 
    RunnerConfigMarshaller<T> 
    +  + +

    +

    +Package compbio.engine.conf Description +

    + +

    +Classes commonly used by both engines. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-tree.html b/website/full_javadoc/compbio/engine/conf/package-tree.html new file mode 100644 index 0000000..460b1b5 --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.engine.conf Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.engine.conf +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/conf/package-use.html b/website/full_javadoc/compbio/engine/conf/package-use.html new file mode 100644 index 0000000..46402ba --- /dev/null +++ b/website/full_javadoc/compbio/engine/conf/package-use.html @@ -0,0 +1,170 @@ + + + + + + +Uses of Package compbio.engine.conf + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.engine.conf

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.conf
    compbio.engine.confClasses commonly used by both engines. 
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.conf used by compbio.engine.conf
    _Key + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html new file mode 100644 index 0000000..4e4459d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/AsyncLocalRunner.html @@ -0,0 +1,402 @@ + + + + + + +AsyncLocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class AsyncLocalRunner

    +
    +java.lang.Object
+  extended by compbio.engine.local.AsyncLocalRunner
+
    +
    +
    All Implemented Interfaces:
    AsyncExecutor
    +
    +
    +
    +
    public final class AsyncLocalRunner
    extends java.lang.Object
    implements AsyncExecutor
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    AsyncLocalRunner() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job.
    + booleancleanup(java.lang.String jobId) + +
    +          Remove all files and a job directory for a jobid.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Query the status of the job
    + ConfiguredExecutable<?>getResults(java.lang.String taskId) + +
    +          Retrieve the results of the job.
    + java.lang.StringgetWorkDirectory(java.lang.String jobId) + +
    +           
    + java.lang.StringsubmitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +AsyncLocalRunner

    +
    +public AsyncLocalRunner()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory(java.lang.String jobId)
    +
    +
    +
    Specified by:
    getWorkDirectory in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - unique job identifier +
    Returns:
    task working directory
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Stop running job. Please not that this method does not guarantee to remove the job directory and files in it. +

    +

    +
    Specified by:
    cancelJob in interface AsyncExecutor
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Query the status of the job +

    +

    +
    Specified by:
    getJobStatus in interface AsyncExecutor
    +
    +
    + +
    Returns:
    The JobStatus object representing the status of the job
    See Also:
    JobStatus
    +
    +
    +
    + +

    +submitJob

    +
    +public java.lang.String submitJob(ConfiguredExecutable<?> executable)
+                           throws JobSubmissionException
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. + All it guarantees that the job will be eventually executed. + The start of execution will depend on the number of jobs in the queue. +

    +

    +
    Specified by:
    submitJob in interface AsyncExecutor
    +
    +
    + +
    Returns:
    unique job identifier +
    Throws: +
    JobSubmissionException - if submission fails. This usually happens due to the problem on a server side.
    +
    +
    +
    + +

    +cleanup

    +
    +public boolean cleanup(java.lang.String jobId)
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Remove all files and a job directory for a jobid. +

    +

    +
    Specified by:
    cleanup in interface AsyncExecutor
    +
    +
    +
    Parameters:
    jobId - +
    Returns:
    +
    +
    +
    + +

    +getResults

    +
    +public ConfiguredExecutable<?> getResults(java.lang.String taskId)
+                                   throws ResultNotAvailableException
    +
    +
    Description copied from interface: AsyncExecutor
    +
    Retrieve the results of the job. Please not that current implementations of this method + blocks if the task is running until the end of the calculation. +

    +

    +
    Specified by:
    getResults in interface AsyncExecutor
    +
    +
    +
    Parameters:
    taskId - job identifier obtained at the job submission +
    Returns:
    ConfiguredExecutable object from which result can be obtained +
    Throws: +
    ResultNotAvailableException - if the result is not available for whatever reason. + Could be due to execution failure, or due to the results being removed from the server at + the time of request.
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html new file mode 100644 index 0000000..421469f --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/ExecutableWrapper.html @@ -0,0 +1,331 @@ + + + + + + +ExecutableWrapper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class ExecutableWrapper

    +
    +java.lang.Object
+  extended by compbio.engine.local.ExecutableWrapper
+
    +
    +
    All Implemented Interfaces:
    java.util.concurrent.Callable<ConfiguredExecutable<?>>
    +
    +
    +
    +
    @Immutable
+public final class ExecutableWrapper
    extends java.lang.Object
    implements java.util.concurrent.Callable<ConfiguredExecutable<?>>
    + + +

    +

    + +

    + + + + + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringPROC_ERR_FILE + +
    +           
    +static java.lang.StringPROC_OUT_FILE + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    + ConfiguredExecutable<?>call() + +
    +          It is vital that output and error streams are captured immediately for + this call() to succeed.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +PROC_OUT_FILE

    +
    +public static final java.lang.String PROC_OUT_FILE
    +
    +
    +
    See Also:
    Constant Field Values
    +
    +
    + +

    +PROC_ERR_FILE

    +
    +public static final java.lang.String PROC_ERR_FILE
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ExecutableWrapper

    +
    +public ExecutableWrapper(ConfiguredExecutable<?> executable,
+                         java.lang.String workDirectory)
+                  throws JobSubmissionException
    +
    +
    + +
    Throws: +
    JobSubmissionException
    +
    + + + + + + + + +
    +Method Detail
    + +

    +call

    +
    +public ConfiguredExecutable<?> call()
+                             throws java.io.IOException
    +
    +
    It is vital that output and error streams are captured immediately for + this call() to succeed. Thus each instance if ExecutableWrapper has 2 its + own thread ready to capture the output. If executor could not execute + capture immediately this could lead to the call method to stale, as + execution could not proceed without output being captured. Every call to + call() method will use 2 threads +

    +

    +
    Specified by:
    call in interface java.util.concurrent.Callable<ConfiguredExecutable<?>>
    +
    +
    + +
    Throws: +
    java.io.IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html new file mode 100644 index 0000000..a4edf4a --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalEngineUtil.html @@ -0,0 +1,335 @@ + + + + + + +LocalEngineUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class LocalEngineUtil

    +
    +java.lang.Object
+  extended by compbio.engine.local.LocalEngineUtil
+
    +
    +
    +
    public final class LocalEngineUtil
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LocalEngineUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static booleancancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String workDirectory) + +
    +           
    +static booleancleanup(ConfiguredExecutable<?> confExecutable) + +
    +           
    +static JobStatusgetJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    +static JobStatusgetRecordedJobStatus(java.lang.String jobId) + +
    +           
    +static ConfiguredExecutable<?>getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +LocalEngineUtil

    +
    +public LocalEngineUtil()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +cancelJob

    +
    +public static boolean cancelJob(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
+                                java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getJobStatus

    +
    +public static JobStatus getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future)
    +
    +
    +
    +
    +
    +
    + +

    +getRecordedJobStatus

    +
    +public static JobStatus getRecordedJobStatus(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +cleanup

    +
    +public static boolean cleanup(ConfiguredExecutable<?> confExecutable)
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public static ConfiguredExecutable<?> getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future,
+                                                 java.lang.String taskId)
+                                          throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html new file mode 100644 index 0000000..9cf5fd7 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalExecutorService.html @@ -0,0 +1,310 @@ + + + + + + +LocalExecutorService + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class LocalExecutorService

    +
    +java.lang.Object
+  extended by java.util.concurrent.AbstractExecutorService
+      extended by java.util.concurrent.ThreadPoolExecutor
+          extended by compbio.engine.local.LocalExecutorService
+
    +
    +
    All Implemented Interfaces:
    java.util.concurrent.Executor, java.util.concurrent.ExecutorService
    +
    +
    +
    +
    public final class LocalExecutorService
    extends java.util.concurrent.ThreadPoolExecutor
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from class java.util.concurrent.ThreadPoolExecutor
    java.util.concurrent.ThreadPoolExecutor.AbortPolicy, java.util.concurrent.ThreadPoolExecutor.CallerRunsPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardOldestPolicy, java.util.concurrent.ThreadPoolExecutor.DiscardPolicy
    +  + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancanAcceptMoreWork() + +
    +          If the Executor queue is empty
    +static LocalExecutorServicegetExecutor() + +
    +          This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally
    +static voidshutDown() + +
    +          This stops all executing processes via interruption.
    +  + + + + + + + +
    Methods inherited from class java.util.concurrent.ThreadPoolExecutor
    allowCoreThreadTimeOut, allowsCoreThreadTimeOut, awaitTermination, execute, getActiveCount, getCompletedTaskCount, getCorePoolSize, getKeepAliveTime, getLargestPoolSize, getMaximumPoolSize, getPoolSize, getQueue, getRejectedExecutionHandler, getTaskCount, getThreadFactory, isShutdown, isTerminated, isTerminating, prestartAllCoreThreads, prestartCoreThread, purge, remove, setCorePoolSize, setKeepAliveTime, setMaximumPoolSize, setRejectedExecutionHandler, setThreadFactory, shutdown, shutdownNow
    +  + + + + + + + +
    Methods inherited from class java.util.concurrent.AbstractExecutorService
    invokeAll, invokeAll, invokeAny, invokeAny, submit, submit, submit
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getExecutor

    +
    +public static LocalExecutorService getExecutor()
    +
    +
    This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally +

    +

    + +
    Returns:
    +
    +
    +
    + +

    +shutDown

    +
    +public static void shutDown()
    +
    +
    This stops all executing processes via interruption. Thus it is vital + that all processes that use this service respond to interruption +

    +

    +
    +
    +
    +
    + +

    +canAcceptMoreWork

    +
    +public boolean canAcceptMoreWork()
    +
    +
    If the Executor queue is empty +

    +

    + +
    Returns:
    true is not all threads are busy, false overwise
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/LocalRunner.html b/website/full_javadoc/compbio/engine/local/LocalRunner.html new file mode 100644 index 0000000..b64d9db --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/LocalRunner.html @@ -0,0 +1,398 @@ + + + + + + +LocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class LocalRunner

    +
    +java.lang.Object
+  extended by compbio.engine.local.LocalRunner
+
    +
    +
    All Implemented Interfaces:
    SyncExecutor
    +
    +
    +
    +
    public final class LocalRunner
    extends java.lang.Object
    implements SyncExecutor
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LocalRunner(ConfiguredExecutable<?> executable) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleancancelJob() + +
    +          Stops running job.
    + booleancleanup() + +
    +          Clean up after the job
    + voidexecuteJob() + +
    +          Execute the job
    + JobStatusgetJobStatus() + +
    +          Query the status of the job by its id.
    + java.lang.StringgetWorkDirectory() + +
    +           
    + ConfiguredExecutable<?>waitForResult() + +
    +          Call to this method block for as long as it is required for an executable to finish its job.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +LocalRunner

    +
    +public LocalRunner(ConfiguredExecutable<?> executable)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getWorkDirectory

    +
    +public java.lang.String getWorkDirectory()
    +
    +
    +
    Specified by:
    getWorkDirectory in interface SyncExecutor
    +
    +
    + +
    Returns:
    working directory if the task
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Stops running job. + Clean up is not performed. +

    +

    +
    Specified by:
    cancelJob in interface SyncExecutor
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Query the status of the job by its id. +

    +

    +
    Specified by:
    getJobStatus in interface SyncExecutor
    +
    +
    + +
    Returns:
    - JobStatus
    +
    +
    +
    + +

    +executeJob

    +
    +public void executeJob()
+                throws JobSubmissionException
    +
    +
    Description copied from interface: SyncExecutor
    +
    Execute the job +

    +

    +
    Specified by:
    executeJob in interface SyncExecutor
    +
    +
    + +
    Throws: +
    JobSubmissionException - if submission fails
    +
    +
    +
    + +

    +waitForResult

    +
    +public ConfiguredExecutable<?> waitForResult()
+                                      throws JobExecutionException
    +
    +
    Description copied from interface: SyncExecutor
    +
    Call to this method block for as long as it is required for an executable to finish its job. + If the calculation has been completed already, the this method returns results immediately. + This could return the result directly, but that would be type unsafe +

    +

    +
    Specified by:
    waitForResult in interface SyncExecutor
    +
    +
    + +
    Returns:
    object from wich the result can be obtained +
    Throws: +
    java.util.concurrent.CancellationException +
    JobExecutionException
    +
    +
    +
    + +

    +cleanup

    +
    +public boolean cleanup()
    +
    +
    Description copied from interface: SyncExecutor
    +
    Clean up after the job +

    +

    +
    Specified by:
    cleanup in interface SyncExecutor
    +
    +
    + +
    Returns:
    true if all the files created by this job have been removed successfully, false otherwise
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/StreamGobbler.html new file mode 100644 index 0000000..4ddf4c6 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/StreamGobbler.html @@ -0,0 +1,226 @@ + + + + + + +StreamGobbler + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class StreamGobbler

    +
    +java.lang.Object
+  extended by compbio.engine.local.StreamGobbler
+
    +
    +
    All Implemented Interfaces:
    java.lang.Runnable
    +
    +
    +
    +
    @ThreadSafe
+public class StreamGobbler
    extends java.lang.Object
    implements java.lang.Runnable
    + + +

    +

    + +

    + + + + + + + + + + + + +
    +Method Summary
    + voidrun() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +run

    +
    +public void run()
    +
    +
    +
    Specified by:
    run in interface java.lang.Runnable
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html new file mode 100644 index 0000000..e10952d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/_TrackingExecutor.html @@ -0,0 +1,427 @@ + + + + + + +_TrackingExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.engine.local +
    +Class _TrackingExecutor

    +
    +java.lang.Object
+  extended by java.util.concurrent.AbstractExecutorService
+      extended by compbio.engine.local._TrackingExecutor
+
    +
    +
    All Implemented Interfaces:
    java.util.concurrent.Executor, java.util.concurrent.ExecutorService
    +
    +
    +
    +
    public class _TrackingExecutor
    extends java.util.concurrent.AbstractExecutorService
    + + +

    +This executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination. For this to work properly Runnables must propagate an + Interruption exceptions, not swallow them, which a good Runnable should do + anyway. + + TODO it may be better to persists task from different place +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _TrackingExecutor(java.util.concurrent.ExecutorService executor) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanawaitTermination(long timeout, + java.util.concurrent.TimeUnit unit) + +
    +           
    + voidexecute(java.lang.Runnable runnable) + +
    +           
    + java.util.ListgetCancelledTasks() + +
    +           
    + booleanisShutdown() + +
    +           
    + booleanisTerminated() + +
    +           
    + voidshutdown() + +
    +           
    + java.util.List<java.lang.Runnable>shutdownNow() + +
    +           
    + + + + + +
    +<T> java.util.concurrent.Future<T>
    +    		submit(java.util.concurrent.Callable<T> task) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.util.concurrent.AbstractExecutorService
    invokeAll, invokeAll, invokeAny, invokeAny, submit, submit
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_TrackingExecutor

    +
    +public _TrackingExecutor(java.util.concurrent.ExecutorService executor)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCancelledTasks

    +
    +public java.util.List getCancelledTasks()
    +
    +
    +
    +
    +
    +
    + +

    +execute

    +
    +public void execute(java.lang.Runnable runnable)
    +
    +
    +
    +
    +
    +
    + +

    +submit

    +
    +public <T> java.util.concurrent.Future<T> submit(java.util.concurrent.Callable<T> task)
    +
    +
    +
    Specified by:
    submit in interface java.util.concurrent.ExecutorService
    Overrides:
    submit in class java.util.concurrent.AbstractExecutorService
    +
    +
    +
    +
    +
    +
    + +

    +awaitTermination

    +
    +public boolean awaitTermination(long timeout,
+                                java.util.concurrent.TimeUnit unit)
+                         throws java.lang.InterruptedException
    +
    +
    + +
    Throws: +
    java.lang.InterruptedException
    +
    +
    +
    + +

    +isShutdown

    +
    +public boolean isShutdown()
    +
    +
    +
    +
    +
    +
    + +

    +isTerminated

    +
    +public boolean isTerminated()
    +
    +
    +
    +
    +
    +
    + +

    +shutdown

    +
    +public void shutdown()
    +
    +
    +
    +
    +
    +
    + +

    +shutdownNow

    +
    +public java.util.List<java.lang.Runnable> shutdownNow()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html new file mode 100644 index 0000000..a5689d9 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/AsyncLocalRunner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.AsyncLocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.local.AsyncLocalRunner

    +
    +No usage of compbio.engine.local.AsyncLocalRunner +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html b/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html new file mode 100644 index 0000000..ecbab56 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/ExecutableWrapper.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.ExecutableWrapper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.local.ExecutableWrapper

    +
    +No usage of compbio.engine.local.ExecutableWrapper +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html b/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html new file mode 100644 index 0000000..2e55194 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/LocalEngineUtil.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.LocalEngineUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.local.LocalEngineUtil

    +
    +No usage of compbio.engine.local.LocalEngineUtil +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html b/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html new file mode 100644 index 0000000..1b52d1f --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/LocalExecutorService.html @@ -0,0 +1,182 @@ + + + + + + +Uses of Class compbio.engine.local.LocalExecutorService + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.engine.local.LocalExecutorService

    +
    + + + + + + + + + +
    +Packages that use LocalExecutorService
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +Uses of LocalExecutorService in compbio.engine.local
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.local that return LocalExecutorService
    +static LocalExecutorServiceLocalExecutorService.getExecutor() + +
    +          This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html b/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html new file mode 100644 index 0000000..c8d8e6b --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/LocalRunner.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.LocalRunner + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.local.LocalRunner

    +
    +No usage of compbio.engine.local.LocalRunner +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html b/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html new file mode 100644 index 0000000..017c86e --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/StreamGobbler.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local.StreamGobbler + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.engine.local.StreamGobbler

    +
    +No usage of compbio.engine.local.StreamGobbler +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html b/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html new file mode 100644 index 0000000..db6bec9 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/class-use/_TrackingExecutor.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.engine.local._TrackingExecutor + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.engine.local._TrackingExecutor

    +
    +No usage of compbio.engine.local._TrackingExecutor +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/package-frame.html b/website/full_javadoc/compbio/engine/local/package-frame.html new file mode 100644 index 0000000..02fb20e --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/package-frame.html @@ -0,0 +1,44 @@ + + + + + + +compbio.engine.local + + + + + + + + + + + +compbio.engine.local + + + + +
    +Classes  + +
    +_TrackingExecutor +
    +AsyncLocalRunner +
    +ExecutableWrapper +
    +LocalEngineUtil +
    +LocalExecutorService +
    +LocalRunner +
    +StreamGobbler
    + + + + diff --git a/website/full_javadoc/compbio/engine/local/package-summary.html b/website/full_javadoc/compbio/engine/local/package-summary.html new file mode 100644 index 0000000..b9dc15d --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/package-summary.html @@ -0,0 +1,207 @@ + + + + + + +compbio.engine.local + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.engine.local +

    +An local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _TrackingExecutorThis executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination.
    AsyncLocalRunner 
    ExecutableWrapper 
    LocalEngineUtil 
    LocalExecutorService 
    LocalRunner 
    StreamGobbler 
    +  + +

    +

    +Package compbio.engine.local Description +

    + +

    +An local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). + Implementation uses Java 6 Executor framework to execute native programmes in parallel in different threads. + Classes in this package depend on the data model classes. + They form a second layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/local/package-tree.html b/website/full_javadoc/compbio/engine/local/package-tree.html new file mode 100644 index 0000000..f34b8b2 --- /dev/null +++ b/website/full_javadoc/compbio/engine/local/package-tree.html @@ -0,0 +1,162 @@ + + + + + + +compbio.engine.local Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.engine.local +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Uses of Package
    compbio.engine.local

    +
    + + + + + + + + + +
    +Packages that use compbio.engine.local
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + + + + +
    +Classes in compbio.engine.local used by compbio.engine.local
    LocalExecutorService + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Interfaces  + +
    +AsyncExecutor +
    +SyncExecutor
    + + + + + + +
    +Classes  + +
    +Cleaner +
    +ClusterJobId +
    +Configurator +
    +FilePuller +
    +Job +
    +LoadBalancer +
    +ProgressGetter +
    +PulledFileCache +
    +SubmissionManager
    + + + + diff --git a/website/full_javadoc/compbio/engine/package-summary.html b/website/full_javadoc/compbio/engine/package-summary.html new file mode 100644 index 0000000..da7acf2 --- /dev/null +++ b/website/full_javadoc/compbio/engine/package-summary.html @@ -0,0 +1,208 @@ + + + + + + +compbio.engine + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.engine +

    + + + + + + + + + + + + + +
    +Interface Summary
    AsyncExecutorAn asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    SyncExecutorSynchronous executor, is an engine to run the Executable synchronously.
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    Cleaner 
    ClusterJobId 
    Configurator 
    FilePuller 
    Job 
    LoadBalancer 
    ProgressGetter 
    PulledFileCache 
    SubmissionManagerSubmit jobs for execution
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/package-tree.html b/website/full_javadoc/compbio/engine/package-tree.html new file mode 100644 index 0000000..7a5f91e --- /dev/null +++ b/website/full_javadoc/compbio/engine/package-tree.html @@ -0,0 +1,159 @@ + + + + + + +compbio.engine Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +

    +Hierarchy For Package compbio.engine +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/engine/package-use.html b/website/full_javadoc/compbio/engine/package-use.html new file mode 100644 index 0000000..0c8ff4d --- /dev/null +++ b/website/full_javadoc/compbio/engine/package-use.html @@ -0,0 +1,274 @@ + + + + + + +Uses of Package compbio.engine + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + +
    +
    +

    +Uses of Package
    compbio.engine

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.engine
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.engine used by compbio.engine
    AsyncExecutor + +
    +          An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    ClusterJobId + +
    +           
    FilePuller + +
    +           
    Job + +
    +           
    SyncExecutor + +
    +          Synchronous executor, is an engine to run the Executable synchronously.
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.engine used by compbio.engine.cluster.drmaa
    AsyncExecutor + +
    +          An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    ClusterJobId + +
    +           
    SyncExecutor + +
    +          Synchronous executor, is an engine to run the Executable synchronously.
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.engine used by compbio.engine.local
    AsyncExecutor + +
    +          An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    SyncExecutor + +
    +          Synchronous executor, is an engine to run the Executable synchronously.
    +  +

    + + + + + + + + +
    +Classes in compbio.engine used by compbio.ws.server
    AsyncExecutor + +
    +          An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/Argument.html b/website/full_javadoc/compbio/metadata/Argument.html new file mode 100644 index 0000000..656cb78 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Argument.html @@ -0,0 +1,327 @@ + + + + + + +Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Interface Argument<T>

    +
    +
    Type Parameters:
    T - executable type
    +
    +
    All Known Implementing Classes:
    Option, Parameter
    +
    +
    +
    +
    public interface Argument<T>
    + + +

    +An unmodifiable view for the options and parameters, with one exception - it + allows to set a value +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    See Also:
    Parameter, +Option
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetDefaultValue() + +
    +           
    + java.lang.StringgetDescription() + +
    +           
    + java.net.URLgetFurtherDetails() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.util.List<java.lang.String>getPossibleValues() + +
    +           
    + voidsetValue(java.lang.String defaultValue) + +
    +          Set default values for the parameter or an option
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getFurtherDetails

    +
    +java.net.URL getFurtherDetails()
    +
    +
    +
    +
    +
    +
    + +

    +getDefaultValue

    +
    +java.lang.String getDefaultValue()
    +
    +
    +
    +
    +
    +
    + +

    +getDescription

    +
    +java.lang.String getDescription()
    +
    +
    +
    +
    +
    +
    + +

    +getName

    +
    +java.lang.String getName()
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +java.util.List<java.lang.String> getPossibleValues()
    +
    +
    + +
    Returns:
    List of values allowed for an Argument
    +
    +
    +
    + +

    +setValue

    +
    +void setValue(java.lang.String defaultValue)
+              throws WrongParameterException
    +
    +
    Set default values for the parameter or an option +

    +

    +
    Parameters:
    defaultValue - the value to be set +
    Throws: +
    WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
    See Also:
    ValueConstrain
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/ChunkHolder.html b/website/full_javadoc/compbio/metadata/ChunkHolder.html new file mode 100644 index 0000000..9b66ead --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ChunkHolder.html @@ -0,0 +1,350 @@ + + + + + + +ChunkHolder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class ChunkHolder

    +
    +java.lang.Object
+  extended by compbio.metadata.ChunkHolder
+
    +
    +
    +
    public class ChunkHolder
    extends java.lang.Object
    + + +

    +Represents a chunk of string data together with the position in a file from + where corresponding to of the data. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ChunkHolder(java.lang.String chunk, + long position) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetChunk() + +
    +           
    + longgetNextPosition() + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ChunkHolder

    +
    +public ChunkHolder(java.lang.String chunk,
+                   long position)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getChunk

    +
    +public java.lang.String getChunk()
    +
    +
    +
    +
    +
    +
    + +

    +getNextPosition

    +
    +public long getNextPosition()
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/JobExecutionException.html b/website/full_javadoc/compbio/metadata/JobExecutionException.html new file mode 100644 index 0000000..6e1b992 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobExecutionException.html @@ -0,0 +1,279 @@ + + + + + + +JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class JobExecutionException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobExecutionException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class JobExecutionException
    extends java.lang.Exception
    + + +

    +JobExecutionException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides DrmaaException +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    JobExecutionException(java.lang.String message) + +
    +           
    JobExecutionException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    JobExecutionException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobExecutionException

    +
    +public JobExecutionException(java.lang.String message)
    +
    +
    +
    + +

    +JobExecutionException

    +
    +public JobExecutionException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +JobExecutionException

    +
    +public JobExecutionException(java.lang.String message,
+                             java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/JobStatus.html b/website/full_javadoc/compbio/metadata/JobStatus.html new file mode 100644 index 0000000..7d716e8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobStatus.html @@ -0,0 +1,465 @@ + + + + + + +JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Enum JobStatus

    +
    +java.lang.Object
+  extended by java.lang.Enum<JobStatus>
+      extended by compbio.metadata.JobStatus
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<JobStatus>
    +
    +
    +
    +
    public enum JobStatus
    extends java.lang.Enum<JobStatus>
    + + +

    +The status of the job. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    CANCELLED + +
    +          Jobs that has been cancelled
    COLLECTED + +
    +          Results has been collected
    FAILED + +
    +          Failed jobs
    FINISHED + +
    +          Finished jobs
    PENDING + +
    +          Jobs which are in the queue and awaiting execution reported for cluster + jobs only
    RUNNING + +
    +          Jobs that are running
    STARTED + +
    +          Job calculation has been started.
    SUBMITTED + +
    +          Job has been submitted.
    UNDEFINED + +
    +          Represents jobs with unknown status
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static JobStatusvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JobStatus[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +PENDING

    +
    +public static final JobStatus PENDING
    +
    +
    Jobs which are in the queue and awaiting execution reported for cluster + jobs only +

    +

    +
    +
    +
    + +

    +RUNNING

    +
    +public static final JobStatus RUNNING
    +
    +
    Jobs that are running +

    +

    +
    +
    +
    + +

    +CANCELLED

    +
    +public static final JobStatus CANCELLED
    +
    +
    Jobs that has been cancelled +

    +

    +
    +
    +
    + +

    +FINISHED

    +
    +public static final JobStatus FINISHED
    +
    +
    Finished jobs +

    +

    +
    +
    +
    + +

    +FAILED

    +
    +public static final JobStatus FAILED
    +
    +
    Failed jobs +

    +

    +
    +
    +
    + +

    +UNDEFINED

    +
    +public static final JobStatus UNDEFINED
    +
    +
    Represents jobs with unknown status +

    +

    +
    +
    +
    + +

    +STARTED

    +
    +public static final JobStatus STARTED
    +
    +
    Job calculation has been started. First status reported by the local + engine +

    +

    +
    +
    +
    + +

    +SUBMITTED

    +
    +public static final JobStatus SUBMITTED
    +
    +
    Job has been submitted. This status is only set for cluster jobs +

    +

    +
    +
    +
    + +

    +COLLECTED

    +
    +public static final JobStatus COLLECTED
    +
    +
    Results has been collected +

    +

    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static JobStatus[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (JobStatus c : JobStatus.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static JobStatus valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/JobSubmissionException.html new file mode 100644 index 0000000..c290dba --- /dev/null +++ b/website/full_javadoc/compbio/metadata/JobSubmissionException.html @@ -0,0 +1,283 @@ + + + + + + +JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class JobSubmissionException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    Direct Known Subclasses:
    LimitExceededException, UnsupportedRuntimeException
    +
    +
    +
    +
    public class JobSubmissionException
    extends java.lang.Exception
    + + +

    +Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException. If + this exception is thrown the task has not been calculated +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    JobSubmissionException(java.lang.String message) + +
    +           
    JobSubmissionException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    JobSubmissionException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +JobSubmissionException

    +
    +public JobSubmissionException(java.lang.String message)
    +
    +
    +
    + +

    +JobSubmissionException

    +
    +public JobSubmissionException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +JobSubmissionException

    +
    +public JobSubmissionException(java.lang.String message,
+                              java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html new file mode 100644 index 0000000..f2f4095 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Limit.html @@ -0,0 +1,459 @@ + + + + + + +Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class Limit<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.Limit<T>
+
    +
    +
    Type Parameters:
    T - the type of an executable for which this limit is defined.
    +
    +
    +
    public class Limit<T>
    extends java.lang.Object
    + + +

    +A value object containing a maximum number of sequences and a maximum average + sequence length for a preset. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date January 2010
    +
    See Also:
    LimitsManager
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    Limit(int seqNumber, + int seqLength, + java.lang.String preset) + +
    +           
    Limit(int seqNumber, + int seqLength, + java.lang.String preset, + boolean isDefault) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + intgetAvgSeqLength() + +
    +           
    +static intgetAvgSequenceLength(java.util.List<FastaSequence> data) + +
    +          Calculates an average sequence length of the dataset
    + java.lang.StringgetPreset() + +
    +           
    + intgetSeqNumber() + +
    +           
    + inthashCode() + +
    +           
    + booleanisDefault() + +
    +           
    + booleanisExceeded(java.util.List<FastaSequence> data) + +
    +          Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Limit

    +
    +public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset)
    +
    +
    +
    + +

    +Limit

    +
    +public Limit(int seqNumber,
+             int seqLength,
+             java.lang.String preset,
+             boolean isDefault)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPreset

    +
    +public java.lang.String getPreset()
    +
    +
    +
    +
    +
    +
    + +

    +getAvgSeqLength

    +
    +public int getAvgSeqLength()
    +
    +
    +
    +
    +
    +
    + +

    +getSeqNumber

    +
    +public int getSeqNumber()
    +
    +
    +
    +
    +
    +
    + +

    +isDefault

    +
    +public boolean isDefault()
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +isExceeded

    +
    +public boolean isExceeded(java.util.List<FastaSequence> data)
    +
    +
    Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit +

    +

    +
    Parameters:
    data - +
    Returns:
    true if a limit is exceeded (what is the dataset is larger then + the limit), false otherwise.
    +
    +
    +
    + +

    +getAvgSequenceLength

    +
    +public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
    +
    +
    Calculates an average sequence length of the dataset +

    +

    +
    Parameters:
    data - +
    Returns:
    an average sequence length in the input dataset
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/LimitExceededException.html b/website/full_javadoc/compbio/metadata/LimitExceededException.html new file mode 100644 index 0000000..910baa8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/LimitExceededException.html @@ -0,0 +1,357 @@ + + + + + + +LimitExceededException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class LimitExceededException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.LimitExceededException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class LimitExceededException
    extends JobSubmissionException
    + + +

    +Thrown if the task larger in size that the limit that applies to the + calculation. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    See Also:
    Limit, +Serialized Form
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitExceededException(java.lang.String message) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + intgetActualNumberofSequences() + +
    +           
    + intgetNumberOfSequencesAllowed() + +
    +           
    + intgetSequenceLenghtActual() + +
    +           
    + intgetSequenceLenghtAllowed() + +
    +           
    +static LimitExceededExceptionnewLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +LimitExceededException

    +
    +public LimitExceededException(java.lang.String message)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +newLimitExceeded

    +
    +public static LimitExceededException newLimitExceeded(Limit<?> limit,
+                                                      java.util.List<FastaSequence> seqs)
    +
    +
    +
    +
    +
    +
    + +

    +getNumberOfSequencesAllowed

    +
    +public int getNumberOfSequencesAllowed()
    +
    +
    +
    +
    +
    +
    + +

    +getActualNumberofSequences

    +
    +public int getActualNumberofSequences()
    +
    +
    +
    +
    +
    +
    + +

    +getSequenceLenghtAllowed

    +
    +public int getSequenceLenghtAllowed()
    +
    +
    +
    +
    +
    +
    + +

    +getSequenceLenghtActual

    +
    +public int getSequenceLenghtActual()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/LimitsManager.html b/website/full_javadoc/compbio/metadata/LimitsManager.html new file mode 100644 index 0000000..88195c6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/LimitsManager.html @@ -0,0 +1,363 @@ + + + + + + +LimitsManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class LimitsManager<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.LimitsManager<T>
+
    +
    +
    Type Parameters:
    T - executable type
    +
    +
    +
    public class LimitsManager<T>
    extends java.lang.Object
    + + +

    +A collection of Limits +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date January 2010
    +
    See Also:
    Limit
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    LimitsManager() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Limit<T>getDefaultLimit() + +
    +           
    + Limit<T>getLimitByName(java.lang.String presetName) + +
    +           
    + java.util.List<Limit<T>>getLimits() + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidvalidate(PresetManager<T> presets) + +
    +          Validate Limits
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +LimitsManager

    +
    +public LimitsManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getLimits

    +
    +public java.util.List<Limit<T>> getLimits()
    +
    +
    + +
    Returns:
    all limits defined for an executable T
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getLimitByName

    +
    +public Limit<T> getLimitByName(java.lang.String presetName)
    +
    +
    +
    Parameters:
    presetName - +
    Returns:
    Limit defined for the executable T and presetName. If no limit is + defined for the presetName then default Limit is returned. If + presetName is empty or null than the default Limit will be + returned. If not limit defined for the type T than NULL will be + returned
    +
    +
    +
    + +

    +getDefaultLimit

    +
    +public Limit<T> getDefaultLimit()
    +
    +
    + +
    Returns:
    the default Limit for an executable type T
    +
    +
    +
    + +

    +validate

    +
    +public void validate(PresetManager<T> presets)
+              throws javax.xml.bind.ValidationException
    +
    +
    Validate Limits +

    +

    +
    Parameters:
    presets - +
    Throws: +
    javax.xml.bind.ValidationException - if any of the Limit defined is found to be invalid. That is + when + + 1) No default limit is defined + + 2) More than 1 default limit is defined + + 3) Limit's preset name does not match any presets for type T
    See Also:
    Limit, +Preset
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/Option.html b/website/full_javadoc/compbio/metadata/Option.html new file mode 100644 index 0000000..1bb99d9 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Option.html @@ -0,0 +1,714 @@ + + + + + + +Option + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class Option<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.Option<T>
+
    +
    +
    Type Parameters:
    T - type of executable
    +
    +
    All Implemented Interfaces:
    Argument<T>
    +
    +
    +
    Direct Known Subclasses:
    Parameter
    +
    +
    +
    +
    public class Option<T>
    extends java.lang.Object
    implements Argument<T>
    + + +

    +Command line option/flag or multiple exclusive options with no value. Example + -protein, -dna, -auto +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Option(java.lang.String name, + java.lang.String description) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
    +          Adds an option to the optionName list
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetDefaultValue() + +
    +          A default value of the option.
    + java.lang.StringgetDescription() + +
    +          A long description of the Option
    + java.net.URLgetFurtherDetails() + +
    +          The URL where further details about the option can be found
    + java.lang.StringgetName() + +
    +          Human readable name of the option
    + java.util.List<java.lang.String>getOptionNames() + +
    +           
    + java.util.List<java.lang.String>getPossibleValues() + +
    +          List of possible optionNames
    + inthashCode() + +
    +           
    + booleanisRequired() + +
    +          Flag that indicated that this option must be specified in the command + line for an executable to run
    + voidsetDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidsetDescription(java.lang.String description) + +
    +           
    + voidsetFurtherDetails(java.net.URL furtherDetails) + +
    +           
    + voidsetName(java.lang.String name) + +
    +           
    + voidsetOptionNames(java.util.Set<java.lang.String> optionNames) + +
    +           
    + voidsetRequired(boolean isRequired) + +
    +           
    + voidsetValue(java.lang.String dValue) + +
    +          Set default values for the parameter or an option
    + java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
    +          Convert the option to the command string.
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Option

    +
    +public Option(java.lang.String name,
+              java.lang.String description)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    Human readable name of the option +

    +

    +
    Specified by:
    getName in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public void setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getDescription

    +
    +public java.lang.String getDescription()
    +
    +
    A long description of the Option +

    +

    +
    Specified by:
    getDescription in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setDescription

    +
    +public void setDescription(java.lang.String description)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getFurtherDetails

    +
    +public java.net.URL getFurtherDetails()
    +
    +
    The URL where further details about the option can be found +

    +

    +
    Specified by:
    getFurtherDetails in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setFurtherDetails

    +
    +public void setFurtherDetails(java.net.URL furtherDetails)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getDefaultValue

    +
    +public java.lang.String getDefaultValue()
    +
    +
    A default value of the option. Defaults to command line argument name + e.g. -auto +

    +

    +
    Specified by:
    getDefaultValue in interface Argument<T>
    +
    +
    +
    +
    +
    +
    + +

    +setDefaultValue

    +
    +public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
    +
    +
    Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

    +

    +
    +
    +
    +
    Parameters:
    defaultVal - +
    Throws: +
    WrongParameterException - is thrown if the defaultValue is not found in optionList
    +
    +
    +
    + +

    +isRequired

    +
    +public boolean isRequired()
    +
    +
    Flag that indicated that this option must be specified in the command + line for an executable to run +

    +

    +
    +
    +
    + +
    Returns:
    true is the option is required, false otherwise
    +
    +
    +
    + +

    +setRequired

    +
    +public void setRequired(boolean isRequired)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getOptionNames

    +
    +public java.util.List<java.lang.String> getOptionNames()
    +
    +
    +
    +
    +
    + +
    Returns:
    List of option names
    +
    +
    +
    + +

    +setOptionNames

    +
    +public void setOptionNames(java.util.Set<java.lang.String> optionNames)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addOptionNames

    +
    +public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
    +
    +
    Adds an option to the optionName list +

    +

    +
    +
    +
    +
    Parameters:
    value - +
    Returns:
    modified optionName list
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toCommand

    +
    +public java.lang.String toCommand(java.lang.String nameValueSeparator)
    +
    +
    Convert the option to the command string. +

    +

    +
    +
    +
    + +
    Returns:
    If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +public java.util.List<java.lang.String> getPossibleValues()
    +
    +
    List of possible optionNames +

    +

    +
    Specified by:
    getPossibleValues in interface Argument<T>
    +
    +
    + +
    Returns:
    List of values allowed for an Argument
    +
    +
    +
    + +

    +setValue

    +
    +public void setValue(java.lang.String dValue)
+              throws WrongParameterException
    +
    +
    Description copied from interface: Argument
    +
    Set default values for the parameter or an option +

    +

    +
    Specified by:
    setValue in interface Argument<T>
    +
    +
    +
    Parameters:
    dValue - the value to be set +
    Throws: +
    WrongParameterException - - when the value to be set is illegal. Wrong value for + numeric parameter is the value defined outside it , for + string type parameter, wrong value is the one which is not + listed in possible values list
    See Also:
    ValueConstrain
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/Parameter.html b/website/full_javadoc/compbio/metadata/Parameter.html new file mode 100644 index 0000000..45505e0 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Parameter.html @@ -0,0 +1,572 @@ + + + + + + +Parameter + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class Parameter<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.Option<T>
+      extended by compbio.metadata.Parameter<T>
+
    +
    +
    All Implemented Interfaces:
    Argument<T>
    +
    +
    +
    +
    public class Parameter<T>
    extends Option<T>
    + + +

    +A single value containing option supported by the web service e.g. + seqType=protein. Where seqType is a optionName and protein is one of + possibleValues +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date November 2009
    +
    See Also:
    Option, +Argument
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Parameter(java.lang.String name, + java.lang.String description) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.Set<java.lang.String>addOptionNames(java.lang.String... value) + +
    +          Adds an option to the optionName list
    + java.util.Set<java.lang.String>addPossibleValues(java.lang.String... value) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.StringgetOptionName() + +
    +           
    + java.util.List<java.lang.String>getPossibleValues() + +
    +          List is more convenient to work with
    + ValueConstraingetValidValue() + +
    +           
    + inthashCode() + +
    +           
    + voidsetDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidsetOptionName(java.lang.String optionName) + +
    +           
    + voidsetOptionNames(java.util.Set<java.lang.String> optionName) + +
    +           
    + voidsetPossibleValues(java.util.Set<java.lang.String> possibleValues) + +
    +           
    + voidsetValidValue(ValueConstrain validValue) + +
    +           
    + java.lang.StringtoCommand(java.lang.String nameValueSeparator) + +
    +          Convert the option to the command string.
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.metadata.Option
    getDefaultValue, getDescription, getFurtherDetails, getName, getOptionNames, isRequired, setDescription, setFurtherDetails, setName, setRequired, setValue
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Parameter

    +
    +public Parameter(java.lang.String name,
+                 java.lang.String description)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getValidValue

    +
    +public ValueConstrain getValidValue()
    +
    +
    +
    +
    +
    +
    + +

    +setValidValue

    +
    +public void setValidValue(ValueConstrain validValue)
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +toCommand

    +
    +public java.lang.String toCommand(java.lang.String nameValueSeparator)
    +
    +
    Description copied from class: Option
    +
    Convert the option to the command string. +

    +

    +
    Overrides:
    toCommand in class Option<T>
    +
    +
    + +
    Returns:
    If only one optionName is defined, than it is returned, if many + option names are defined, then the defaultValue is returned. + Option must have a default value if there are many optionNames to + be valid.
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +getPossibleValues

    +
    +public java.util.List<java.lang.String> getPossibleValues()
    +
    +
    List is more convenient to work with +

    +

    +
    Specified by:
    getPossibleValues in interface Argument<T>
    Overrides:
    getPossibleValues in class Option<T>
    +
    +
    + +
    Returns:
    List of String
    +
    +
    +
    + +

    +setPossibleValues

    +
    +public void setPossibleValues(java.util.Set<java.lang.String> possibleValues)
    +
    +
    +
    +
    +
    +
    + +

    +addPossibleValues

    +
    +public java.util.Set<java.lang.String> addPossibleValues(java.lang.String... value)
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +setOptionNames

    +
    +public void setOptionNames(java.util.Set<java.lang.String> optionName)
    +
    +
    +
    Overrides:
    setOptionNames in class Option<T>
    +
    +
    +
    +
    +
    +
    + +

    +addOptionNames

    +
    +public java.util.Set<java.lang.String> addOptionNames(java.lang.String... value)
    +
    +
    Description copied from class: Option
    +
    Adds an option to the optionName list +

    +

    +
    Overrides:
    addOptionNames in class Option<T>
    +
    +
    + +
    Returns:
    modified optionName list
    +
    +
    +
    + +

    +getOptionName

    +
    +public java.lang.String getOptionName()
    +
    +
    +
    +
    +
    +
    + +

    +setOptionName

    +
    +public void setOptionName(java.lang.String optionName)
    +
    +
    +
    +
    +
    +
    + +

    +setDefaultValue

    +
    +public void setDefaultValue(java.lang.String defaultVal)
+                     throws WrongParameterException
    +
    +
    Description copied from class: Option
    +
    Sets one of the values defined in optionList as default. Attempting set + the value not listed there will result in WrongParameter exception +

    +

    +
    Overrides:
    setDefaultValue in class Option<T>
    +
    +
    + +
    Throws: +
    WrongParameterException - is thrown if the defaultValue is not found in optionList
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/Preset.html b/website/full_javadoc/compbio/metadata/Preset.html new file mode 100644 index 0000000..2995b06 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/Preset.html @@ -0,0 +1,455 @@ + + + + + + +Preset + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class Preset<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.Preset<T>
+
    +
    +
    Type Parameters:
    T - executable type
    +
    +
    +
    public class Preset<T>
    extends java.lang.Object
    + + +

    +Collection of Options and Parameters with their values +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    See Also:
    Option, +Parameter
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Preset() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.util.List<Option<T>>getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + java.lang.StringgetDescription() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.util.List<java.lang.String>getOptions() + +
    +           
    + inthashCode() + +
    +           
    + voidsetDescription(java.lang.String description) + +
    +           
    + voidsetName(java.lang.String name) + +
    +           
    + voidsetOptions(java.util.List<java.lang.String> option) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Preset

    +
    +public Preset()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setOptions

    +
    +public void setOptions(java.util.List<java.lang.String> option)
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public void setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    + +

    +setDescription

    +
    +public void setDescription(java.lang.String description)
    +
    +
    +
    +
    +
    +
    + +

    +getOptions

    +
    +public java.util.List<java.lang.String> getOptions()
    +
    +
    + +
    Returns:
    a List of Options as a String
    +
    +
    +
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    + +
    Returns:
    - name of the Preset
    +
    +
    +
    + +

    +getDescription

    +
    +public java.lang.String getDescription()
    +
    +
    + +
    Returns:
    - a long description of the Preset
    +
    +
    +
    + +

    +getArguments

    +
    +public java.util.List<Option<T>> getArguments(RunnerConfig<T> rconfig)
+                                       throws WrongParameterException
    +
    +
    Converts list of options as String to type Option +

    +

    +
    Parameters:
    rconfig - +
    Returns:
    List of Options +
    Throws: +
    WrongParameterException - if the value of the parameter is invalid @see + Parameter
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/PresetManager.html b/website/full_javadoc/compbio/metadata/PresetManager.html new file mode 100644 index 0000000..17b792a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/PresetManager.html @@ -0,0 +1,428 @@ + + + + + + +PresetManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class PresetManager<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.PresetManager<T>
+
    +
    +
    Type Parameters:
    T - type of executable.
    +
    +
    +
    public class PresetManager<T>
    extends java.lang.Object
    + + +

    +Collection of presets and methods to manipulate them @see Preset +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date December 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringLOCAL_ENGINE_LIMIT_PRESET + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    PresetManager() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Preset<T>getPresetByName(java.lang.String presetName) + +
    +           
    + java.util.List<Preset<T>>getPresets() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + voidsetPresets(java.util.List<Preset<T>> presets) + +
    +           
    + voidsetRunnerClassName(java.lang.String runnerClassName) + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidvalidate(RunnerConfig<T> options) + +
    +          Checks whether preset option and parameter are defined in RunnerConfig + object.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +LOCAL_ENGINE_LIMIT_PRESET

    +
    +public static final java.lang.String LOCAL_ENGINE_LIMIT_PRESET
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +PresetManager

    +
    +public PresetManager()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getPresets

    +
    +public java.util.List<Preset<T>> getPresets()
    +
    +
    +
    +
    +
    +
    + +

    +setPresets

    +
    +public void setPresets(java.util.List<Preset<T>> presets)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    + +
    Returns:
    fully qualified class name of type T
    +
    +
    +
    + +

    +setRunnerClassName

    +
    +public void setRunnerClassName(java.lang.String runnerClassName)
    +
    +
    +
    +
    +
    +
    + +

    +getPresetByName

    +
    +public Preset<T> getPresetByName(java.lang.String presetName)
    +
    +
    +
    Parameters:
    presetName - +
    Returns:
    preset by its name, null if no preset found
    +
    +
    +
    + +

    +validate

    +
    +public void validate(RunnerConfig<T> options)
+              throws javax.xml.bind.ValidationException
    +
    +
    Checks whether preset option and parameter are defined in RunnerConfig + object. + + TODO handle parameters with values properly! +

    +

    + +
    Throws: +
    javax.xml.bind.ValidationException - if preset is found to be invalid.
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html new file mode 100644 index 0000000..c0d8b57 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ResultNotAvailableException.html @@ -0,0 +1,280 @@ + + + + + + +ResultNotAvailableException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class ResultNotAvailableException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.ResultNotAvailableException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class ResultNotAvailableException
    extends java.lang.Exception
    + + +

    +ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained. For cluster execution it hides lower level exceptions + like DrmaaException +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    ResultNotAvailableException(java.lang.String message) + +
    +           
    ResultNotAvailableException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    ResultNotAvailableException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ResultNotAvailableException

    +
    +public ResultNotAvailableException(java.lang.String message)
    +
    +
    +
    + +

    +ResultNotAvailableException

    +
    +public ResultNotAvailableException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +ResultNotAvailableException

    +
    +public ResultNotAvailableException(java.lang.String message,
+                                   java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/RunnerConfig.html b/website/full_javadoc/compbio/metadata/RunnerConfig.html new file mode 100644 index 0000000..7f59fd8 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/RunnerConfig.html @@ -0,0 +1,640 @@ + + + + + + +RunnerConfig + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class RunnerConfig<T>

    +
    +java.lang.Object
+  extended by compbio.metadata.RunnerConfig<T>
+
    +
    +
    Type Parameters:
    T - type of an Executable
    +
    +
    +
    @NotThreadSafe
+public class RunnerConfig<T>
    extends java.lang.Object
    + + +

    +The list of Parameters and Options supported by executable. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    RunnerConfig() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + voidaddOption(Option<T> option) + +
    +           
    + voidaddParameter(Parameter<T> param) + +
    +           
    + RunnerConfig<T>copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    + booleanequals(java.lang.Object obj) + +
    +           
    + Option<T>getArgument(java.lang.String name) + +
    +          Returns the argument by its name if found, NULL otherwise
    + Option<T>getArgumentByOptionName(java.lang.String optionName) + +
    +          Returns the argument by option name, NULL if the argument is not found
    + java.util.List<Option<T>>getArguments() + +
    +           
    + java.util.List<Option<T>>getOptions() + +
    +           
    + java.util.List<Parameter<T>>getParameters() + +
    +           
    + java.lang.StringgetPrmSeparator() + +
    +           
    + java.lang.StringgetRunnerClassName() + +
    +           
    + booleanremoveArgument(java.lang.String name) + +
    +          Removes the argument Argument if found.
    + booleanremoveArgumentByOptionName(java.lang.String optionName) + +
    +          Removes the argument
    + voidsetOptions(java.util.List<Option<T>> parameters) + +
    +           
    + voidsetParameters(java.util.List<Parameter<T>> parameters) + +
    +           
    + voidsetPrmSeparator(java.lang.String prmSeparator) + +
    +           
    + voidsetRunnerClassName(java.lang.String runnerClassName) + +
    +           
    + java.lang.StringtoString() + +
    +           
    + voidvalidate() + +
    +          Validate the arguments
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +RunnerConfig

    +
    +public RunnerConfig()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +copyAndValidateRConfig

    +
    +public RunnerConfig<T> copyAndValidateRConfig(RunnerConfig<?> runnerConf)
    +
    +
    +
    +
    +
    +
    + +

    +getOptions

    +
    +public java.util.List<Option<T>> getOptions()
    +
    +
    + +
    Returns:
    list of Option supported by type T
    +
    +
    +
    + +

    +addParameter

    +
    +public void addParameter(Parameter<T> param)
    +
    +
    +
    +
    +
    +
    + +

    +addOption

    +
    +public void addOption(Option<T> option)
    +
    +
    +
    +
    +
    +
    + +

    +getArguments

    +
    +public java.util.List<Option<T>> getArguments()
    +
    +
    + +
    Returns:
    list of Option and Parameter supported by type T
    +
    +
    +
    + +

    +getPrmSeparator

    +
    +public java.lang.String getPrmSeparator()
    +
    +
    + +
    Returns:
    name value separator character
    +
    +
    +
    + +

    +setPrmSeparator

    +
    +public void setPrmSeparator(java.lang.String prmSeparator)
    +
    +
    +
    +
    +
    +
    + +

    +setOptions

    +
    +public void setOptions(java.util.List<Option<T>> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getRunnerClassName

    +
    +public java.lang.String getRunnerClassName()
    +
    +
    + +
    Returns:
    fully qualified class name for type T
    +
    +
    +
    + +

    +setRunnerClassName

    +
    +public void setRunnerClassName(java.lang.String runnerClassName)
    +
    +
    +
    +
    +
    +
    + +

    +setParameters

    +
    +public void setParameters(java.util.List<Parameter<T>> parameters)
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public java.util.List<Parameter<T>> getParameters()
    +
    +
    + +
    Returns:
    List of Parameter supported by type T.
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +getArgument

    +
    +public Option<T> getArgument(java.lang.String name)
    +
    +
    Returns the argument by its name if found, NULL otherwise +

    +

    +
    Parameters:
    name - +
    Returns:
    Argument
    +
    +
    +
    + +

    +removeArgument

    +
    +public boolean removeArgument(java.lang.String name)
    +
    +
    Removes the argument Argument if found. +

    +

    +
    Parameters:
    name - of the argument +
    Returns:
    true if argument was removed, false otherwise
    +
    +
    +
    + +

    +getArgumentByOptionName

    +
    +public Option<T> getArgumentByOptionName(java.lang.String optionName)
    +
    +
    Returns the argument by option name, NULL if the argument is not found +

    +

    +
    Parameters:
    optionName - - the name of the option +
    Returns:
    Option
    +
    +
    +
    + +

    +removeArgumentByOptionName

    +
    +public boolean removeArgumentByOptionName(java.lang.String optionName)
    +
    +
    Removes the argument +

    +

    +
    Parameters:
    optionName - +
    Returns:
    true if argument with optionName exists and was removed, false + otherwise
    +
    +
    +
    + +

    +validate

    +
    +public void validate()
+              throws javax.xml.bind.ValidationException
    +
    +
    Validate the arguments +

    +

    + +
    Throws: +
    javax.xml.bind.ValidationException - if any of the arguments found invalid which is when +
    +
  • Parameter value outside ValueConstrain boundary
    • +
  • Parameter name is not listed in possible values
    • +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html new file mode 100644 index 0000000..b7d4950 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/UnsupportedRuntimeException.html @@ -0,0 +1,265 @@ + + + + + + +UnsupportedRuntimeException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class UnsupportedRuntimeException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.JobSubmissionException
+              extended by compbio.metadata.UnsupportedRuntimeException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class UnsupportedRuntimeException
    extends JobSubmissionException
    + + +

    +Indicates that the server could not execute native executables. e.g. If Mafft + (unix executable) is asked to be run on Windows. In context of JABAWS this + exception indicates that the service is deployed but is not able to run. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    UnsupportedRuntimeException(java.lang.String message) + +
    +           
    UnsupportedRuntimeException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(java.lang.String message)
    +
    +
    +
    + +

    +UnsupportedRuntimeException

    +
    +public UnsupportedRuntimeException(java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html new file mode 100644 index 0000000..62a7160 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ValueConstrain.Type.html @@ -0,0 +1,325 @@ + + + + + + +ValueConstrain.Type + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Enum ValueConstrain.Type

    +
    +java.lang.Object
+  extended by java.lang.Enum<ValueConstrain.Type>
+      extended by compbio.metadata.ValueConstrain.Type
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<ValueConstrain.Type>
    +
    +
    +
    Enclosing class:
    ValueConstrain
    +
    +
    +
    +
    public static enum ValueConstrain.Type
    extends java.lang.Enum<ValueConstrain.Type>
    + + +

    +

    + +

    + + + + + + + + + + + + + +
    +Enum Constant Summary
    Float + +
    +           
    Integer + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static ValueConstrain.TypevalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +Integer

    +
    +public static final ValueConstrain.Type Integer
    +
    +
    +
    +
    +
    + +

    +Float

    +
    +public static final ValueConstrain.Type Float
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static ValueConstrain.Type[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (ValueConstrain.Type c : ValueConstrain.Type.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static ValueConstrain.Type valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/ValueConstrain.html b/website/full_javadoc/compbio/metadata/ValueConstrain.html new file mode 100644 index 0000000..0d924f6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/ValueConstrain.html @@ -0,0 +1,440 @@ + + + + + + +ValueConstrain + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class ValueConstrain

    +
    +java.lang.Object
+  extended by compbio.metadata.ValueConstrain
+
    +
    +
    +
    public class ValueConstrain
    extends java.lang.Object
    + + +

    +The type and the lower and upper boundaries for numerical value. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date November 2009
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classValueConstrain.Type + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ValueConstrain() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + java.lang.NumbergetMax() + +
    +           
    + java.lang.NumbergetMin() + +
    +           
    + ValueConstrain.TypegetType() + +
    +           
    + inthashCode() + +
    +           
    + voidsetMax(java.lang.String max) + +
    +           
    + voidsetMin(java.lang.String min) + +
    +           
    + voidsetType(ValueConstrain.Type type) + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ValueConstrain

    +
    +public ValueConstrain()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getType

    +
    +public ValueConstrain.Type getType()
    +
    +
    +
    +
    +
    +
    + +

    +setType

    +
    +public void setType(ValueConstrain.Type type)
    +
    +
    +
    +
    +
    +
    + +

    +getMax

    +
    +public java.lang.Number getMax()
    +
    +
    +
    +
    +
    +
    + +

    +setMax

    +
    +public void setMax(java.lang.String max)
    +
    +
    +
    +
    +
    +
    + +

    +getMin

    +
    +public java.lang.Number getMin()
    +
    +
    +
    +
    +
    +
    + +

    +setMin

    +
    +public void setMin(java.lang.String min)
    +
    +
    +
    +
    +
    +
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/WrongParameterException.html b/website/full_javadoc/compbio/metadata/WrongParameterException.html new file mode 100644 index 0000000..9d95892 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/WrongParameterException.html @@ -0,0 +1,294 @@ + + + + + + +WrongParameterException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.metadata +
    +Class WrongParameterException

    +
    +java.lang.Object
+  extended by java.lang.Throwable
+      extended by java.lang.Exception
+          extended by compbio.metadata.WrongParameterException
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable
    +
    +
    +
    +
    public class WrongParameterException
    extends java.lang.Exception
    + + +

    +WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value. +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date October 2009
    +
    See Also:
    Serialized Form
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Constructor Summary
    WrongParameterException(Option<?> option) + +
    +           
    WrongParameterException(java.lang.String message) + +
    +           
    WrongParameterException(java.lang.String message, + java.lang.Throwable cause) + +
    +           
    WrongParameterException(java.lang.Throwable cause) + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Throwable
    fillInStackTrace, getCause, getLocalizedMessage, getMessage, getStackTrace, initCause, printStackTrace, printStackTrace, printStackTrace, setStackTrace, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WrongParameterException

    +
    +public WrongParameterException(Option<?> option)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.String message)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.Throwable cause)
    +
    +
    +
    + +

    +WrongParameterException

    +
    +public WrongParameterException(java.lang.String message,
+                               java.lang.Throwable cause)
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Argument.html b/website/full_javadoc/compbio/metadata/class-use/Argument.html new file mode 100644 index 0000000..11f5c1a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Argument.html @@ -0,0 +1,189 @@ + + + + + + +Uses of Interface compbio.metadata.Argument + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Interface
    compbio.metadata.Argument

    +
    + + + + + + + + + +
    +Packages that use Argument
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of Argument in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Classes in compbio.metadata that implement Argument
    + classOption<T> + +
    +          Command line option/flag or multiple exclusive options with no value.
    + classParameter<T> + +
    +          A single value containing option supported by the web service e.g.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html new file mode 100644 index 0000000..30abc70 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ChunkHolder.html @@ -0,0 +1,356 @@ + + + + + + +Uses of Class compbio.metadata.ChunkHolder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.ChunkHolder

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use ChunkHolder
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return ChunkHolder
    + ChunkHolderMsaWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return ChunkHolder
    + ChunkHolderPullFileResponse.getReturn() + +
    +           
    + ChunkHolderPullExecStatisticsResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type ChunkHolder
    + voidPullFileResponse.setReturn(ChunkHolder _return) + +
    +           
    + voidPullExecStatisticsResponse.setReturn(ChunkHolder _return) + +
    +           
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return ChunkHolder
    + ChunkHolderFilePuller.pull(long position) + +
    +           
    +static ChunkHolderProgressGetter.pull(java.lang.String file, + long position) + +
    +           
    +  +

    + + + + + +
    +Uses of ChunkHolder in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return ChunkHolder
    + ChunkHolderTcoffeeWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderProbconsWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderMuscleWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderMafftWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    + ChunkHolderClustalWS.pullExecStatistics(java.lang.String jobId, + long position) + +
    +           
    +static ChunkHolderWSUtil.pullFile(java.lang.String jobId, + long position) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html b/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html new file mode 100644 index 0000000..2efb5f4 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobExecutionException.html @@ -0,0 +1,257 @@ + + + + + + +Uses of Class compbio.metadata.JobExecutionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.metadata.JobExecutionException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use JobExecutionException
    compbio.engine  
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    +  +

    + + + + + +
    +Uses of JobExecutionException in compbio.engine
    +  +

    + + + + + + + + + +
    Methods in compbio.engine that throw JobExecutionException
    + ConfiguredExecutable<?>SyncExecutor.waitForResult() + +
    +          Call to this method block for as long as it is required for an executable to finish its job.
    +  +

    + + + + + +
    +Uses of JobExecutionException in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that throw JobExecutionException
    + org.ggf.drmaa.JobInfoJobRunner.getJobInfo() + +
    +          This method will block before the calculation has completed and then + return the object containing a job execution statistics
    + ConfiguredExecutable<?>JobRunner.waitForResult() + +
    +           
    +static org.ggf.drmaa.JobInfoClusterUtil.waitForResult(ClusterSession csession, + java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of JobExecutionException in compbio.engine.local
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.local that throw JobExecutionException
    + ConfiguredExecutable<?>LocalRunner.waitForResult() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobStatus.html b/website/full_javadoc/compbio/metadata/class-use/JobStatus.html new file mode 100644 index 0000000..227a5b0 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobStatus.html @@ -0,0 +1,501 @@ + + + + + + +Uses of Class compbio.metadata.JobStatus + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +

    +Uses of Class
    compbio.metadata.JobStatus

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use JobStatus
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return JobStatus
    + JobStatusMsaWS.getJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return JobStatus
    + JobStatusGetJobStatusResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type JobStatus
    + voidGetJobStatusResponse.setReturn(JobStatus _return) + +
    +           
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.engine
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine that return JobStatus
    + JobStatusSyncExecutor.getJobStatus() + +
    +          Query the status of the job by its id.
    + JobStatusAsyncExecutor.getJobStatus(java.lang.String jobId) + +
    +          Query the status of the job
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.engine.client
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.client with parameters of type JobStatus
    +static booleanUtil.isMarked(java.lang.String workDirectory, + JobStatus marker) + +
    +           
    +static booleanUtil.writeMarker(java.lang.String workDirectory, + JobStatus fileType) + +
    +           
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that return JobStatus
    + JobStatusJobRunner.getJobStatus() + +
    +           
    + JobStatusAsyncJobRunner.getJobStatus(java.lang.String jobId) + +
    +          This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.engine.local
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.local that return JobStatus
    + JobStatusLocalRunner.getJobStatus() + +
    +           
    +static JobStatusLocalEngineUtil.getJobStatus(java.util.concurrent.Future<ConfiguredExecutable<?>> future) + +
    +           
    + JobStatusAsyncLocalRunner.getJobStatus(java.lang.String jobId) + +
    +           
    +static JobStatusLocalEngineUtil.getRecordedJobStatus(java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return JobStatus
    +static JobStatusJobStatus.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static JobStatus[]JobStatus.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + +
    +Uses of JobStatus in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return JobStatus
    +static JobStatusWSUtil.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusTcoffeeWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusProbconsWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusMuscleWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusMafftWS.getJobStatus(java.lang.String jobId) + +
    +           
    + JobStatusClustalWS.getJobStatus(java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html b/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html new file mode 100644 index 0000000..1e1329f --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/JobSubmissionException.html @@ -0,0 +1,651 @@ + + + + + + +Uses of Class compbio.metadata.JobSubmissionException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.JobSubmissionException

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use JobSubmissionException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw JobSubmissionException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.engine
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine that throw JobSubmissionException
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + Executable.ExecProvider provider) + +
    +           
    +static + + + + +
    +<T> ConfiguredExecutable<T>
    +    		Configurator.configureExecutable(Executable<T> executable, + java.util.List<FastaSequence> dataSet) + +
    +           
    + voidSyncExecutor.executeJob() + +
    +          Execute the job
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable) + +
    +           
    +static SyncExecutorConfigurator.getSyncEngine(ConfiguredExecutable<?> executable, + Executable.ExecProvider provider) + +
    +           
    + java.lang.StringAsyncExecutor.submitJob(ConfiguredExecutable<?> executable) + +
    +          Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.engine.client
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that throw JobSubmissionException
    + java.lang.StringConfiguredExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that throw JobSubmissionException
    + voidJobRunner.executeJob() + +
    +           
    +static JobRunnerJobRunner.getInstance(ConfiguredExecutable<?> executable) + +
    +           
    + java.lang.StringAsyncJobRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.cluster.drmaa that throw JobSubmissionException
    JobRunner(ConfiguredExecutable<?> confExec) + +
    +           
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.engine.local
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.local that throw JobSubmissionException
    + voidLocalRunner.executeJob() + +
    +           
    + java.lang.StringAsyncLocalRunner.submitJob(ConfiguredExecutable<?> executable) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.engine.local that throw JobSubmissionException
    ExecutableWrapper(ConfiguredExecutable<?> executable, + java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Subclasses of JobSubmissionException in compbio.metadata
    + classLimitExceededException + +
    +          Thrown if the task larger in size that the limit that applies to the + calculation.
    + classUnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    +  +

    + + + + + +
    +Uses of JobSubmissionException in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw JobSubmissionException
    + java.lang.StringTcoffeeWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringProbconsWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMuscleWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringMafftWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    + java.lang.StringClustalWS.align(java.util.List<FastaSequence> sequences) + +
    +           
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Limit.html b/website/full_javadoc/compbio/metadata/class-use/Limit.html new file mode 100644 index 0000000..fa7eced --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Limit.html @@ -0,0 +1,570 @@ + + + + + + +Uses of Class compbio.metadata.Limit + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    + + + +
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    +

    +Uses of Class
    compbio.metadata.Limit

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Limit
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return Limit
    + Limit<T>MsaWS.getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    +  +

    + + + + + +
    +Uses of Limit in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return Limit
    + LimitGetLimitResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type Limit
    + voidGetLimitResponse.setReturn(Limit _return) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.engine.client
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return Limit
    + Limit<T>Executable.getLimit(java.lang.String presetName) + +
    +           
    + Limit<T>ConfExecutable.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.metadata
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Limit
    + Limit<T>LimitsManager.getDefaultLimit() + +
    +           
    + Limit<T>LimitsManager.getLimitByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Limit
    + java.util.List<Limit<T>>LimitsManager.getLimits() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Limit
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return Limit
    + Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Limit
    + Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Limit
    + Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) + +
    +           
    + Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Probcons>Probcons.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Muscle>Muscle.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Mafft>Mafft.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return Limit
    + Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + +
    +Uses of Limit in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return Limit
    + Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Probcons>ProbconsWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Muscle>MuscleWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<Mafft>MafftWS.getLimit(java.lang.String presetName) + +
    +           
    + Limit<ClustalW>ClustalWS.getLimit(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type Limit
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html new file mode 100644 index 0000000..22163d6 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/LimitExceededException.html @@ -0,0 +1,270 @@ + + + + + + +Uses of Class compbio.metadata.LimitExceededException + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.LimitExceededException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use LimitExceededException
    compbio.data.msa  
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw LimitExceededException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return LimitExceededException
    +static LimitExceededExceptionLimitExceededException.newLimitExceeded(Limit<?> limit, + java.util.List<FastaSequence> seqs) + +
    +           
    +  +

    + + + + + +
    +Uses of LimitExceededException in compbio.ws.server
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.server that throw LimitExceededException
    +static + + + + +
    +<T> java.lang.String
    +    		WSUtil.align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html new file mode 100644 index 0000000..1bbf5d5 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/LimitsManager.html @@ -0,0 +1,502 @@ + + + + + + +Uses of Class compbio.metadata.LimitsManager + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    +
    +

    +Uses of Class
    compbio.metadata.LimitsManager

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use LimitsManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return LimitsManager
    + LimitsManager<T>MsaWS.getLimits() + +
    +          List Limits supported by a web service.
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return LimitsManager
    + LimitsManagerGetLimitsResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type LimitsManager
    + voidGetLimitsResponse.setReturn(LimitsManager _return) + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that return LimitsManager
    + LimitsManager<T>Executable.getLimits() + +
    +           
    + LimitsManager<T>ConfExecutable.getLimits() + +
    +           
    +static + + + + +
    +<V> LimitsManager<V>
    +    		ConfExecutable.getRunnerLimits(java.lang.Class<? extends Executable<V>> clazz) + +
    +          This method should be executed once and result of its execution reused.
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner that return LimitsManager
    + LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() + +
    +           
    +static + + + + +
    +<T> LimitsManager<T>
    +    		Util.getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return LimitsManager
    + LimitsManager<NetNglyc>NetNglyc.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return LimitsManager
    + LimitsManager<Tcoffee>Tcoffee.getLimits() + +
    +           
    + LimitsManager<ClustalW>ClustalW.getLimits() + +
    +           
    + LimitsManager<Probcons>Probcons.getLimits() + +
    +           
    + LimitsManager<Muscle>Muscle.getLimits() + +
    +           
    + LimitsManager<Mafft>Mafft.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that return LimitsManager
    + LimitsManager<PsiBlast>PsiBlast.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of LimitsManager in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return LimitsManager
    + LimitsManager<Tcoffee>TcoffeeWS.getLimits() + +
    +           
    + LimitsManager<Probcons>ProbconsWS.getLimits() + +
    +           
    + LimitsManager<Muscle>MuscleWS.getLimits() + +
    +           
    + LimitsManager<Mafft>MafftWS.getLimits() + +
    +           
    + LimitsManager<ClustalW>ClustalWS.getLimits() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Option.html b/website/full_javadoc/compbio/metadata/class-use/Option.html new file mode 100644 index 0000000..1defb5a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Option.html @@ -0,0 +1,539 @@ + + + + + + +Uses of Class compbio.metadata.Option + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.Option

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Option
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa
    +  +

    + + + + + + + + + +
    Method parameters in compbio.data.msa with type arguments of type Option
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    +  +

    + + + + + +
    +Uses of Option in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return types with arguments of type Option
    + java.util.List<Option>CustomAlign.getOptions() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.data.msa.jaxws with type arguments of type Option
    + voidCustomAlign.setOptions(java.util.List<Option> options) + +
    +           
    +  +

    + + + + + +
    +Uses of Option in compbio.engine.client
    +  +

    + + + + + + + + + +
    Method parameters in compbio.engine.client with type arguments of type Option
    +static + + + + +
    +<T> CommandBuilder<T>
    +    		CommandBuilder.newCommandBuilder(java.util.List<? extends Option<T>> arguments, + java.lang.String nameValueSeparator) + +
    +          This produces the same result as getCommands method.
    +  +

    + + + + + +
    +Uses of Option in compbio.metadata
    +  +

    + + + + + + + + + +
    Subclasses of Option in compbio.metadata
    + classParameter<T> + +
    +          A single value containing option supported by the web service e.g.
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.metadata that return Option
    + Option<T>RunnerConfig.getArgument(java.lang.String name) + +
    +          Returns the argument by its name if found, NULL otherwise
    + Option<T>RunnerConfig.getArgumentByOptionName(java.lang.String optionName) + +
    +          Returns the argument by option name, NULL if the argument is not found
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Option
    + java.util.List<Option<T>>RunnerConfig.getArguments() + +
    +           
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + java.util.List<Option<T>>RunnerConfig.getOptions() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Option
    + voidRunnerConfig.addOption(Option<T> option) + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Option
    + voidRunnerConfig.setOptions(java.util.List<Option<T>> parameters) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.metadata with parameters of type Option
    WrongParameterException(Option<?> option) + +
    +           
    +  +

    + + + + + +
    +Uses of Option in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return types with arguments of type Option
    + java.util.List<Option<?>>OptionCombinator.getAllOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Option
    + java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments) + +
    +           
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    + java.util.List<java.lang.String>OptionCombinator.optionsToCommandString(java.util.List<Option<?>> options) + +
    +           
    +  +

    + + + + + +
    +Uses of Option in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Option
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    +static + + + + +
    +<T> java.util.List<java.lang.String>
    +    		WSUtil.getCommands(java.util.List<Option<T>> options, + java.lang.String keyValueSeparator) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.Parameter

    +
    + + + + + + + + + + + + + +
    +Packages that use Parameter
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    +  +

    + + + + + +
    +Uses of Parameter in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Parameter
    + java.util.List<Parameter<T>>RunnerConfig.getParameters() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type Parameter
    + voidRunnerConfig.addParameter(Parameter<T> param) + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Parameter
    + voidRunnerConfig.setParameters(java.util.List<Parameter<T>> parameters) + +
    +           
    +  +

    + + + + + +
    +Uses of Parameter in compbio.runner
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner that return types with arguments of type Parameter
    + java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithBorderValues(boolean minValue) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>OptionCombinator.getAllConstrainedParametersWithRandomValues() + +
    +           
    + java.util.List<Parameter<?>>OptionCombinator.getAllParameters() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.runner with type arguments of type Parameter
    + java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.String> prmValue) + +
    +           
    + java.util.List<java.lang.String>OptionCombinator.parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.String> prmValue) + +
    +           
    +  +

    +

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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/Preset.html b/website/full_javadoc/compbio/metadata/class-use/Preset.html new file mode 100644 index 0000000..e8f8abe --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/Preset.html @@ -0,0 +1,354 @@ + + + + + + +Uses of Class compbio.metadata.Preset + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.Preset

    +
    + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use Preset
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa with parameters of type Preset
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of Preset in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return Preset
    + PresetPresetAlign.getPreset() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type Preset
    + voidPresetAlign.setPreset(Preset preset) + +
    +           
    +  +

    + + + + + +
    +Uses of Preset in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return Preset
    + Preset<T>PresetManager.getPresetByName(java.lang.String presetName) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return types with arguments of type Preset
    + java.util.List<Preset<T>>PresetManager.getPresets() + +
    +           
    +  +

    + + + + + + + + + +
    Method parameters in compbio.metadata with type arguments of type Preset
    + voidPresetManager.setPresets(java.util.List<Preset<T>> presets) + +
    +           
    +  +

    + + + + + +
    +Uses of Preset in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server with parameters of type Preset
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/PresetManager.html b/website/full_javadoc/compbio/metadata/class-use/PresetManager.html new file mode 100644 index 0000000..c6c458a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/PresetManager.html @@ -0,0 +1,388 @@ + + + + + + +Uses of Class compbio.metadata.PresetManager + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.metadata.PresetManager

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use PresetManager
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return PresetManager
    + PresetManager<T>MsaWS.getPresets() + +
    +          Get presets supported by a web service
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return PresetManager
    + PresetManagerGetPresetsResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type PresetManager
    + voidGetPresetsResponse.setReturn(PresetManager _return) + +
    +           
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.engine.client
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that return PresetManager
    +static + + + + +
    +<V> PresetManager<V>
    +    		ConfExecutable.getRunnerPresets(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type PresetManager
    + voidLimitsManager.validate(PresetManager<T> presets) + +
    +          Validate Limits
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return PresetManager
    +static + + + + +
    +<T> PresetManager<T>
    +    		Util.getPresets(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +  +

    + + + + + +
    +Uses of PresetManager in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return PresetManager
    + PresetManager<Tcoffee>TcoffeeWS.getPresets() + +
    +           
    + PresetManager<Probcons>ProbconsWS.getPresets() + +
    +           
    + PresetManager<Muscle>MuscleWS.getPresets() + +
    +           
    + PresetManager<Mafft>MafftWS.getPresets() + +
    +           
    + PresetManager<ClustalW>ClustalWS.getPresets() + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.ResultNotAvailableException

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use ResultNotAvailableException
    compbio.data.msa  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that throw ResultNotAvailableException
    + AlignmentMsaWS.getResult(java.lang.String jobId) + +
    +          Return the result of the job.
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine
    +  +

    + + + + + + + + + +
    Methods in compbio.engine that throw ResultNotAvailableException
    + ConfiguredExecutable<?>AsyncExecutor.getResults(java.lang.String jobId) + +
    +          Retrieve the results of the job.
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine.client
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.engine.client that throw ResultNotAvailableException
    + + + + + +
    +<V> V
    +    		ConfiguredExecutable.getResults() + +
    +           
    + + + + + +
    +<V> V
    +    		ConfExecutable.getResults() + +
    +           
    + + + + + +
    +<V> V
    +    		Executable.getResults(java.lang.String directory) + +
    +           
    + + + + + +
    +<V> V
    +    		ConfExecutable.getResults(java.lang.String directory) + +
    +           
    +static ConfiguredExecutable<?>Util.loadExecutable(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine.cluster.drmaa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.cluster.drmaa that throw ResultNotAvailableException
    + ConfiguredExecutable<?>ClusterSession.getResults(java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncJobRunner.getResults(java.lang.String jobId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.engine.local
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.engine.local that throw ResultNotAvailableException
    +static ConfiguredExecutable<?>LocalEngineUtil.getResults(java.util.concurrent.Future<ConfiguredExecutable<?>> future, + java.lang.String taskId) + +
    +           
    + ConfiguredExecutable<?>AsyncLocalRunner.getResults(java.lang.String taskId) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that throw ResultNotAvailableException
    + AlignmentTcoffee.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentClustalW.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentProbcons.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMuscle.getResults(java.lang.String workDirectory) + +
    +           
    + AlignmentMafft.getResults(java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.runner.psiblast
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.psiblast that throw ResultNotAvailableException
    + + + + + +
    +<V> V
    +    		PsiBlast.getResults(java.lang.String directory) + +
    +           
    +  +

    + + + + + +
    +Uses of ResultNotAvailableException in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw ResultNotAvailableException
    + AlignmentTcoffeeWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentProbconsWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMuscleWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentMafftWS.getResult(java.lang.String jobId) + +
    +           
    + AlignmentClustalWS.getResult(java.lang.String jobId) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html b/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html new file mode 100644 index 0000000..26548ba --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/RunnerConfig.html @@ -0,0 +1,452 @@ + + + + + + +Uses of Class compbio.metadata.RunnerConfig + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.RunnerConfig

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use RunnerConfig
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.data.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa that return RunnerConfig
    + RunnerConfig<T>MsaWS.getRunnerOptions() + +
    +          Get options supported by a web service
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.data.msa.jaxws
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws that return RunnerConfig
    + RunnerConfigGetRunnerOptionsResponse.getReturn() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.data.msa.jaxws with parameters of type RunnerConfig
    + voidGetRunnerOptionsResponse.setReturn(RunnerConfig _return) + +
    +           
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.engine.client
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that return RunnerConfig
    +static + + + + +
    +<V> RunnerConfig<V>
    +    		ConfExecutable.getRunnerOptions(java.lang.Class<? extends Executable<V>> clazz) + +
    +           
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata with parameters of type RunnerConfig
    + RunnerConfig<T>RunnerConfig.copyAndValidateRConfig(RunnerConfig<?> runnerConf) + +
    +           
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidPresetManager.validate(RunnerConfig<T> options) + +
    +          Checks whether preset option and parameter are defined in RunnerConfig + object.
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.runner
    +  +

    + + + + + + + + + +
    Methods in compbio.runner that return RunnerConfig
    +static + + + + +
    +<T> RunnerConfig<T>
    +    		Util.getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.runner with parameters of type RunnerConfig
    +static java.util.List<java.lang.String>OptionCombinator.argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +  +

    + + + + + + + + +
    Constructors in compbio.runner with parameters of type RunnerConfig
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +  +

    + + + + + +
    +Uses of RunnerConfig in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return RunnerConfig
    + RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Muscle>MuscleWS.getRunnerOptions() + +
    +           
    + RunnerConfig<Mafft>MafftWS.getRunnerOptions() + +
    +           
    + RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() + +
    +           
    +  +

    +

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    +Uses of Class
    compbio.metadata.UnsupportedRuntimeException

    +
    + + + + + + + + + + + + + +
    +Packages that use UnsupportedRuntimeException
    compbio.data.msa  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw UnsupportedRuntimeException
    + java.lang.StringMsaWS.align(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of UnsupportedRuntimeException in compbio.engine.client
    +  +

    + + + + + + + + + +
    Methods in compbio.engine.client that throw UnsupportedRuntimeException
    + java.lang.StringConfExecutable.getCommand(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html new file mode 100644 index 0000000..41624ef --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.Type.html @@ -0,0 +1,214 @@ + + + + + + +Uses of Class compbio.metadata.ValueConstrain.Type + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.ValueConstrain.Type

    +
    + + + + + + + + + +
    +Packages that use ValueConstrain.Type
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain.Type in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain.Type
    + ValueConstrain.TypeValueConstrain.getType() + +
    +           
    +static ValueConstrain.TypeValueConstrain.Type.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static ValueConstrain.Type[]ValueConstrain.Type.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain.Type
    + voidValueConstrain.setType(ValueConstrain.Type type) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html new file mode 100644 index 0000000..7c8825a --- /dev/null +++ b/website/full_javadoc/compbio/metadata/class-use/ValueConstrain.html @@ -0,0 +1,197 @@ + + + + + + +Uses of Class compbio.metadata.ValueConstrain + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.ValueConstrain

    +
    + + + + + + + + + +
    +Packages that use ValueConstrain
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    +  +

    + + + + + +
    +Uses of ValueConstrain in compbio.metadata
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata that return ValueConstrain
    + ValueConstrainParameter.getValidValue() + +
    +           
    +  +

    + + + + + + + + + +
    Methods in compbio.metadata with parameters of type ValueConstrain
    + voidParameter.setValidValue(ValueConstrain validValue) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.metadata.WrongParameterException

    +
    + + + + + + + + + + + + + + + + + +
    +Packages that use WrongParameterException
    compbio.data.msa  
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.data.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.data.msa that throw WrongParameterException
    + java.lang.StringMsaWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<T>> options) + +
    +          Align a list of sequences with options.
    + java.lang.StringMsaWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<T> preset) + +
    +          Align a list of sequences with preset.
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.metadata
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.metadata that throw WrongParameterException
    + java.util.List<Option<T>>Preset.getArguments(RunnerConfig<T> rconfig) + +
    +          Converts list of options as String to type Option
    + voidParameter.setDefaultValue(java.lang.String defaultVal) + +
    +           
    + voidOption.setDefaultValue(java.lang.String defaultVal) + +
    +          Sets one of the values defined in optionList as default.
    + voidArgument.setValue(java.lang.String defaultValue) + +
    +          Set default values for the parameter or an option
    + voidOption.setValue(java.lang.String dValue) + +
    +           
    +  +

    + + + + + +
    +Uses of WrongParameterException in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that throw WrongParameterException
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

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    + + + diff --git a/website/full_javadoc/compbio/metadata/package-frame.html b/website/full_javadoc/compbio/metadata/package-frame.html new file mode 100644 index 0000000..1739396 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-frame.html @@ -0,0 +1,93 @@ + + + + + + +compbio.metadata + + + + + + + + + + + +compbio.metadata + + + + +
    +Interfaces  + +
    +Argument
    + + + + + + +
    +Classes  + +
    +ChunkHolder +
    +Limit +
    +LimitsManager +
    +Option +
    +Parameter +
    +Preset +
    +PresetManager +
    +RunnerConfig +
    +ValueConstrain
    + + + + + + +
    +Enums  + +
    +JobStatus +
    +ValueConstrain.Type
    + + + + + + +
    +Exceptions  + +
    +JobExecutionException +
    +JobSubmissionException +
    +LimitExceededException +
    +ResultNotAvailableException +
    +UnsupportedRuntimeException +
    +WrongParameterException
    + + + + diff --git a/website/full_javadoc/compbio/metadata/package-summary.html b/website/full_javadoc/compbio/metadata/package-summary.html new file mode 100644 index 0000000..5f5b66b --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-summary.html @@ -0,0 +1,286 @@ + + + + + + +compbio.metadata + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    +

    +Package compbio.metadata +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. +

    +See: +
    +          Description +

    + + + + + + + + + +
    +Interface Summary
    Argument<T>An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    ChunkHolderRepresents a chunk of string data together with the position in a file from + where corresponding to of the data.
    Limit<T>A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager<T>A collection of Limits
    Option<T>Command line option/flag or multiple exclusive options with no value.
    Parameter<T>A single value containing option supported by the web service e.g.
    Preset<T>Collection of Options and Parameters with their values
    PresetManager<T>Collection of presets and methods to manipulate them @see Preset
    RunnerConfig<T>The list of Parameters and Options supported by executable.
    ValueConstrainThe type and the lower and upper boundaries for numerical value.
    +  + +

    + + + + + + + + + + + + + +
    +Enum Summary
    JobStatusThe status of the job.
    ValueConstrain.Type 
    +  + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Exception Summary
    JobExecutionExceptionJobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobSubmissionExceptionException for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    LimitExceededExceptionThrown if the task larger in size that the limit that applies to the + calculation.
    ResultNotAvailableExceptionResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    UnsupportedRuntimeExceptionIndicates that the server could not execute native executables.
    WrongParameterExceptionWrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  + +

    +

    +Package compbio.metadata Description +

    + +

    +A meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. + They form a base layer of Jalview Web Services v2. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/metadata/package-tree.html b/website/full_javadoc/compbio/metadata/package-tree.html new file mode 100644 index 0000000..3d95bb3 --- /dev/null +++ b/website/full_javadoc/compbio/metadata/package-tree.html @@ -0,0 +1,178 @@ + + + + + + +compbio.metadata Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Hierarchy For Package compbio.metadata +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +

    +Interface Hierarchy +

    + +

    +Enum Hierarchy +

    +
      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
      +
    +
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    + + + + + + + + + + + + + + + +
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    +Uses of Package
    compbio.metadata

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Packages that use compbio.metadata
    compbio.data.msa  
    compbio.data.msa.jaxws  
    compbio.engine  
    compbio.engine.clientClasses and interfaces representing an input for engines. 
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters. 
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes). 
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project. 
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.runner.psiblast  
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.data.msa
    ChunkHolder + +
    +          Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          Thrown if the task larger in size that the limit that applies to the + calculation.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.data.msa.jaxws
    ChunkHolder + +
    +          Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    JobStatus + +
    +          The status of the job.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.engine
    ChunkHolder + +
    +          Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    JobExecutionException + +
    +          JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.engine.client
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    UnsupportedRuntimeException + +
    +          Indicates that the server could not execute native executables.
    +  +

    + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.engine.cluster.drmaa
    JobExecutionException + +
    +          JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.engine.local
    JobExecutionException + +
    +          JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.metadata
    Argument + +
    +          An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          Thrown if the task larger in size that the limit that applies to the + calculation.
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Parameter + +
    +          A single value containing option supported by the web service e.g.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    ValueConstrain + +
    +          The type and the lower and upper boundaries for numerical value.
    ValueConstrain.Type + +
    +           
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.runner
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Parameter + +
    +          A single value containing option supported by the web service e.g.
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    +  +

    + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.runner._impl
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.runner.msa
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.runner.psiblast
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitsManager + +
    +          A collection of Limits
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.metadata used by compbio.ws.server
    ChunkHolder + +
    +          Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    JobStatus + +
    +          The status of the job.
    JobSubmissionException + +
    +          Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    Limit + +
    +          A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    LimitExceededException + +
    +          Thrown if the task larger in size that the limit that applies to the + calculation.
    LimitsManager + +
    +          A collection of Limits
    Option + +
    +          Command line option/flag or multiple exclusive options with no value.
    Preset + +
    +          Collection of Options and Parameters with their values
    PresetManager + +
    +          Collection of presets and methods to manipulate them @see Preset
    ResultNotAvailableException + +
    +          ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    RunnerConfig + +
    +          The list of Parameters and Options supported by executable.
    WrongParameterException + +
    +          WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html new file mode 100644 index 0000000..f15b429 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/BlastParser.html @@ -0,0 +1,259 @@ + + + + + + +BlastParser + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.pipeline._jpred +
    +Class BlastParser

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.BlastParser
+
    +
    +
    +
    public class BlastParser
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    BlastParser() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +          args[0] is assumed to be the name of a Blast output file
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +BlastParser

    +
    +public BlastParser()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.io.FileNotFoundException,
+                        javax.xml.stream.XMLStreamException
    +
    +
    args[0] is assumed to be the name of a Blast output file +

    +

    + +
    Throws: +
    javax.xml.stream.XMLStreamException +
    java.io.FileNotFoundException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html new file mode 100644 index 0000000..8669156 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/Jpred4.html @@ -0,0 +1,277 @@ + + + + + + +Jpred4 + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.pipeline._jpred +
    +Class Jpred4

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.Jpred4
+
    +
    +
    +
    public class Jpred4
    extends java.lang.Object
    + + +

    +jpred --sequence OR --alignment [--db + ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] + + jpred4 --sequence The path to the sequence (in FASTA format) you + want to predict OR + + [--alignment ] The alignment which to use for prediction + + [--profile=] + + [--db ] Database to use for PSI-BLAST querying. Default: uniref90 ( + /homes/www-jpred/databases/uniref90.filt) Please note that database must be + psi-blast indexed + + [--pred-nohits] Toggle allowing Jpred to make predictions even when there are + no PSI-BLAST hits. + + [--logLevel=(ERROR|INFO|DEBUG)] one of ERROR, INFO, DEBUG [--help] +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Jpred4() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    + voidrunPsiBlast() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Jpred4

    +
    +public Jpred4()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +runPsiBlast

    +
    +public void runPsiBlast()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/PScore.html new file mode 100644 index 0000000..668b60b --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/PScore.html @@ -0,0 +1,299 @@ + + + + + + +PScore + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.pipeline._jpred +
    +Class PScore

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.PScore
+
    +
    +
    +
    public class PScore
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    PScore() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + booleanequals(java.lang.Object obj) + +
    +           
    + inthashCode() + +
    +           
    + java.lang.StringtoString() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PScore

    +
    +public PScore()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +equals

    +
    +public boolean equals(java.lang.Object obj)
    +
    +
    +
    Overrides:
    equals in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +hashCode

    +
    +public int hashCode()
    +
    +
    +
    Overrides:
    hashCode in class java.lang.Object
    +
    +
    +
    +
    +
    +
    + +

    +toString

    +
    +public java.lang.String toString()
    +
    +
    +
    Overrides:
    toString in class java.lang.Object
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html new file mode 100644 index 0000000..3200264 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/Pairwise.html @@ -0,0 +1,257 @@ + + + + + + +Pairwise + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.pipeline._jpred +
    +Class Pairwise

    +
    +java.lang.Object
+  extended by compbio.pipeline._jpred.Pairwise
+
    +
    +
    +
    public class Pairwise
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    Pairwise(java.util.List<FastaSequence> sequences) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Pairwise

    +
    +public Pairwise(java.util.List<FastaSequence> sequences)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static final void main(java.lang.String[] args)
+                       throws java.io.FileNotFoundException,
+                              java.io.IOException
    +
    +
    + +
    Throws: +
    java.io.FileNotFoundException +
    java.io.IOException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html new file mode 100644 index 0000000..5380574 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/BlastParser.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.BlastParser + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.BlastParser

    +
    +No usage of compbio.pipeline._jpred.BlastParser +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html new file mode 100644 index 0000000..e70f570 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Jpred4.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.Jpred4 + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.Jpred4

    +
    +No usage of compbio.pipeline._jpred.Jpred4 +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html new file mode 100644 index 0000000..26263db --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/PScore.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.PScore + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.PScore

    +
    +No usage of compbio.pipeline._jpred.PScore +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html new file mode 100644 index 0000000..754a87e --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/class-use/Pairwise.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.pipeline._jpred.Pairwise + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.pipeline._jpred.Pairwise

    +
    +No usage of compbio.pipeline._jpred.Pairwise +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html b/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html new file mode 100644 index 0000000..f22d288 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.pipeline._jpred + + + + + + + + + + + +compbio.pipeline._jpred + + + + +
    +Classes  + +
    +BlastParser +
    +Jpred4 +
    +Pairwise +
    +PScore
    + + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html new file mode 100644 index 0000000..06bf2f8 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-summary.html @@ -0,0 +1,179 @@ + + + + + + +compbio.pipeline._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.pipeline._jpred +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    BlastParser 
    Jpred4jpred --sequence OR --alignment [--db + ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] + + jpred4 --sequence The path to the sequence (in FASTA format) you + want to predict OR + + [--alignment ] The alignment which to use for prediction + + [--profile=] + + [--db ] Database to use for PSI-BLAST querying.
    Pairwise 
    PScore 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html b/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html new file mode 100644 index 0000000..e907ee7 --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.pipeline._jpred Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use   Tree  Deprecated  Index  Help 
    +    		 + +
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    +

    +Hierarchy For Package compbio.pipeline._jpred +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/pipeline/_jpred/package-use.html b/website/full_javadoc/compbio/pipeline/_jpred/package-use.html new file mode 100644 index 0000000..90ca61e --- /dev/null +++ b/website/full_javadoc/compbio/pipeline/_jpred/package-use.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Package compbio.pipeline._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Package
    compbio.pipeline._jpred

    +
    +No usage of compbio.pipeline._jpred +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/OptionCombinator.html b/website/full_javadoc/compbio/runner/OptionCombinator.html new file mode 100644 index 0000000..69a5662 --- /dev/null +++ b/website/full_javadoc/compbio/runner/OptionCombinator.html @@ -0,0 +1,421 @@ + + + + + + +OptionCombinator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner +
    +Class OptionCombinator

    +
    +java.lang.Object
+  extended by compbio.runner.OptionCombinator
+
    +
    +
    +
    @Immutable
+public final class OptionCombinator
    extends java.lang.Object
    + + +

    +This class solve the following problems. Given the RunnerConfig + + 1) generate a valid option string with all options and parameters in it + + 2) Permute all possible combinations of options order and parameters values +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments) + +
    +           
    +static java.util.List<java.lang.String>argumentsToCommandString(java.util.List<? extends Option<?>> arguments, + RunnerConfig<? extends Executable<?>> rconfig) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithBorderValues(boolean minValue) + +
    +           
    + java.util.Map<Parameter<?>,java.lang.String>getAllConstrainedParametersWithRandomValues() + +
    +           
    + java.util.List<Option<?>>getAllOptions() + +
    +           
    + java.util.List<Parameter<?>>getAllParameters() + +
    +           
    + java.util.List<java.lang.String>getOptionsAtRandom() + +
    +           
    + java.util.List<java.lang.String>optionsToCommandString(java.util.List<Option<?>> options) + +
    +           
    + java.util.List<java.lang.String>parametersToCommandString(java.util.List<Parameter<?>> orderedList, + java.util.Map<Parameter<?>,java.lang.String> prmValue) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +OptionCombinator

    +
    +public OptionCombinator(RunnerConfig<? extends Executable<?>> rconfig)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +optionsToCommandString

    +
    +public java.util.List<java.lang.String> optionsToCommandString(java.util.List<Option<?>> options)
    +
    +
    +
    +
    +
    +
    + +

    +getOptionsAtRandom

    +
    +public java.util.List<java.lang.String> getOptionsAtRandom()
    +
    +
    +
    +
    +
    +
    + +

    +getAllOptions

    +
    +public java.util.List<Option<?>> getAllOptions()
    +
    +
    +
    +
    +
    +
    + +

    +getAllParameters

    +
    +public java.util.List<Parameter<?>> getAllParameters()
    +
    +
    +
    +
    +
    +
    + +

    +argumentsToCommandString

    +
    +public java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments)
    +
    +
    +
    +
    +
    +
    + +

    +argumentsToCommandString

    +
    +public static java.util.List<java.lang.String> argumentsToCommandString(java.util.List<? extends Option<?>> arguments,
+                                                                        RunnerConfig<? extends Executable<?>> rconfig)
    +
    +
    +
    +
    +
    +
    + +

    +parametersToCommandString

    +
    +public java.util.List<java.lang.String> parametersToCommandString(java.util.List<Parameter<?>> orderedList,
+                                                                  java.util.Map<Parameter<?>,java.lang.String> prmValue)
    +
    +
    +
    +
    +
    +
    + +

    +getAllConstrainedParametersWithBorderValues

    +
    +public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithBorderValues(boolean minValue)
    +
    +
    +
    +
    +
    +
    + +

    +getAllConstrainedParametersWithRandomValues

    +
    +public java.util.Map<Parameter<?>,java.lang.String> getAllConstrainedParametersWithRandomValues()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/Util.html b/website/full_javadoc/compbio/runner/Util.html new file mode 100644 index 0000000..d09afc7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/Util.html @@ -0,0 +1,409 @@ + + + + + + +Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner +
    +Class Util

    +
    +java.lang.Object
+  extended by compbio.runner.Util
+
    +
    +
    +
    public final class Util
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringSPACE + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Util() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> LimitsManager<T>
    +    		getLimits(java.lang.Class<? extends Executable<T>> clazz) + +
    +          For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then
    +static + + + + +
    +<T> PresetManager<T>
    +    		getPresets(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static + + + + +
    +<T> RunnerConfig<T>
    +    		getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz) + +
    +           
    +static AlignmentreadClustalFile(java.lang.String workDirectory, + java.lang.String clustFile) + +
    +           
    +static voidwriteInput(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<?> exec) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +SPACE

    +
    +public static final java.lang.String SPACE
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Util

    +
    +public Util()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getLimits

    +
    +public static <T> LimitsManager<T> getLimits(java.lang.Class<? extends Executable<T>> clazz)
    +
    +
    For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then +

    +

    +
    Parameters:
    rconfig - +
    Returns:
    public static List toOptionString(RunnerConfig + rconfig) { String option = ""; List options = new + ArrayList(); for (Parameter par : + rconfig.getParameters()) { if (par.getPossibleValues().isEmpty()) + { option = par.getOptionName(); } else { option = + par.getOptionName() + "=" + par.getPossibleValues().get(0); } // + separate options options.add(option); } return options; }
    +
    +
    +
    + +

    +getSupportedOptions

    +
    +public static <T> RunnerConfig<T> getSupportedOptions(java.lang.Class<? extends Executable<T>> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +getPresets

    +
    +public static <T> PresetManager<T> getPresets(java.lang.Class<? extends Executable<T>> clazz)
    +
    +
    +
    +
    +
    +
    + +

    +readClustalFile

    +
    +public static final Alignment readClustalFile(java.lang.String workDirectory,
+                                              java.lang.String clustFile)
+                                       throws UnknownFileFormatException,
+                                              java.io.IOException,
+                                              java.io.FileNotFoundException,
+                                              java.lang.NullPointerException
    +
    +
    + +
    Throws: +
    UnknownFileFormatException +
    java.io.IOException +
    java.io.FileNotFoundException +
    java.lang.NullPointerException
    +
    +
    +
    + +

    +writeInput

    +
    +public static void writeInput(java.util.List<FastaSequence> sequences,
+                              ConfiguredExecutable<?> exec)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html new file mode 100644 index 0000000..05a5ca7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_NativeSpecHelper.html @@ -0,0 +1,347 @@ + + + + + + +_NativeSpecHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner +
    +Class _NativeSpecHelper

    +
    +java.lang.Object
+  extended by compbio.runner._NativeSpecHelper
+
    +
    +
    +
    public class _NativeSpecHelper
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + +
    +Constructor Summary
    _NativeSpecHelper(int requiredMemory) + +
    +           
    _NativeSpecHelper(int requiredMemory, + int maxCalculationTime) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + _QueuegetApproprieteQueue() + +
    +           
    + java.lang.StringgetNativeSpec() + +
    +           
    + java.lang.StringgetQueue() + +
    +           
    + voidsetQueue(java.lang.String queue) + +
    +           
    + voidsetRequiredMemory(int memory) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_NativeSpecHelper

    +
    +public _NativeSpecHelper(int requiredMemory)
    +
    +
    +
    + +

    +_NativeSpecHelper

    +
    +public _NativeSpecHelper(int requiredMemory,
+                         int maxCalculationTime)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setRequiredMemory

    +
    +public void setRequiredMemory(int memory)
    +
    +
    +
    +
    +
    +
    + +

    +setQueue

    +
    +public void setQueue(java.lang.String queue)
    +
    +
    +
    +
    +
    +
    + +

    +getQueue

    +
    +public java.lang.String getQueue()
    +
    +
    +
    +
    +
    +
    + +

    +getNativeSpec

    +
    +public java.lang.String getNativeSpec()
+                               throws java.net.UnknownServiceException
    +
    +
    + +
    Throws: +
    java.net.UnknownServiceException
    +
    +
    +
    + +

    +getApproprieteQueue

    +
    +public _Queue getApproprieteQueue()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html new file mode 100644 index 0000000..ff0efa8 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_SkeletalCommandBuilder.html @@ -0,0 +1,586 @@ + + + + + + +_SkeletalCommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner +
    +Class _SkeletalCommandBuilder

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    Direct Known Subclasses:
    BlastAll, Disembl, Mcl, OB, PSIBlast, Ronn, RPSBlast
    +
    +
    +
    +
    public abstract class _SkeletalCommandBuilder
    extends java.lang.Object
    implements Executable<_SkeletalCommandBuilder>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    _SkeletalCommandBuilder() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + _SkeletalCommandBuilderaddParameter(java.lang.String parameter) + +
    +           
    + _SkeletalCommandBuilderaddParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + _SkeletalCommandBuilderaddParameters(java.lang.String[] parameters) + +
    +           
    + java.lang.StringgetEmail() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + Limit<_SkeletalCommandBuilder>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<_SkeletalCommandBuilder>getLimits() + +
    +           
    + java.lang.StringgetName() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<_SkeletalCommandBuilder>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    + _SkeletalCommandBuildersetEmail(java.lang.String email) + +
    +           
    + _SkeletalCommandBuildersetName(java.lang.String name) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getInput
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_SkeletalCommandBuilder

    +
    +public _SkeletalCommandBuilder()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setEmail

    +
    +public _SkeletalCommandBuilder setEmail(java.lang.String email)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +setName

    +
    +public _SkeletalCommandBuilder setName(java.lang.String name)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getName

    +
    +public java.lang.String getName()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getEmail

    +
    +public java.lang.String getEmail()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public _SkeletalCommandBuilder addParameters(java.lang.String[] parameters)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public _SkeletalCommandBuilder addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Description copied from interface: Executable
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Specified by:
    addParameters in interface Executable<_SkeletalCommandBuilder>
    +
    +
    + +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<_SkeletalCommandBuilder> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +addParameter

    +
    +public _SkeletalCommandBuilder addParameter(java.lang.String parameter)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
    +
    +
    +
    Specified by:
    getResults in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<_SkeletalCommandBuilder> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<_SkeletalCommandBuilder> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/BlastAll.html new file mode 100644 index 0000000..2faddc5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/BlastAll.html @@ -0,0 +1,360 @@ + + + + + + +BlastAll + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class BlastAll

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.BlastAll
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class BlastAll
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    BlastAll(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + booleanremoveOutput(java.lang.String outfile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +BlastAll

    +
    +public BlastAll(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +removeOutput

    +
    +public boolean removeOutput(java.lang.String outfile)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html new file mode 100644 index 0000000..0dfb3cf --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/BlastParameters.html @@ -0,0 +1,200 @@ + + + + + + +BlastParameters + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class BlastParameters

    +
    +java.lang.Object
+  extended by compbio.runner._impl.BlastParameters
+
    +
    +
    +
    public class BlastParameters
    extends java.lang.Object
    + + +

    +Utility class for common Blast parameters +

    + +

    +

    +
    Author:
    +
    pvtroshin + TODO
    +
    +
    + +

    + + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + +

    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/Disembl.html b/website/full_javadoc/compbio/runner/_impl/Disembl.html new file mode 100644 index 0000000..9c5d600 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Disembl.html @@ -0,0 +1,379 @@ + + + + + + +Disembl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class Disembl

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.Disembl
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class Disembl
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    Disembl(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Disembl

    +
    +public Disembl(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestArgs

    +
    +public static java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/Environment.html b/website/full_javadoc/compbio/runner/_impl/Environment.html new file mode 100644 index 0000000..bc7399c --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Environment.html @@ -0,0 +1,265 @@ + + + + + + +Environment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class Environment

    +
    +java.lang.Object
+  extended by compbio.runner._impl.Environment
+
    +
    +
    +
    public final class Environment
    extends java.lang.Object
    + + +

    +This is utility class to encapsulate environmental variables like directory paths +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static java.lang.StringgetBlastBinDir() + +
    +           
    +static java.lang.StringgetBlastDatabasesDir() + +
    +           
    +static java.lang.StringgetRPSBlastDatabasesDir() + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getBlastBinDir

    +
    +public static java.lang.String getBlastBinDir()
    +
    +
    +
    +
    +
    +
    + +

    +getBlastDatabasesDir

    +
    +public static final java.lang.String getBlastDatabasesDir()
    +
    +
    +
    +
    +
    +
    + +

    +getRPSBlastDatabasesDir

    +
    +public static final java.lang.String getRPSBlastDatabasesDir()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/Mcl.html b/website/full_javadoc/compbio/runner/_impl/Mcl.html new file mode 100644 index 0000000..c5c546f --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Mcl.html @@ -0,0 +1,379 @@ + + + + + + +Mcl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class Mcl

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.Mcl
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class Mcl
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    Mcl(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +static java.util.List<java.lang.String>getTestParams() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Mcl

    +
    +public Mcl(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestParams

    +
    +public static java.util.List<java.lang.String> getTestParams()
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html new file mode 100644 index 0000000..418085d --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/NetNglyc.html @@ -0,0 +1,552 @@ + + + + + + +NetNglyc + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class NetNglyc

    +
    +java.lang.Object
+  extended by compbio.runner._impl.NetNglyc
+
    +
    +
    All Implemented Interfaces:
    Executable<NetNglyc>
    +
    +
    +
    +
    public class NetNglyc
    extends java.lang.Object
    implements Executable<NetNglyc>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    NetNglyc() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + NetNglycaddParameters(java.util.List<java.lang.String> parameters) + +
    +          Adds parameter to the list of parameters for a native executable
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetError() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + Limit<NetNglyc>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<NetNglyc>getLimits() + +
    +           
    + java.lang.StringgetOutput() + +
    +           
    + CommandBuilder<NetNglyc>getParameters(Executable.ExecProvider provider) + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    +static java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    + Executable<?>loadRunConfiguration(RunConfiguration rconfig) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +NetNglyc

    +
    +public NetNglyc()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getParameters

    +
    +public CommandBuilder<NetNglyc> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getTestArgs

    +
    +public static java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public NetNglyc addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Description copied from interface: Executable
    +
    Adds parameter to the list of parameters for a native executable +

    +

    +
    Specified by:
    addParameters in interface Executable<NetNglyc>
    +
    +
    + +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    Specified by:
    getCreatedFiles in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    Specified by:
    getInput in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
    +
    +
    +
    Specified by:
    getResults in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +loadRunConfiguration

    +
    +public Executable<?> loadRunConfiguration(RunConfiguration rconfig)
    +
    +
    +
    Specified by:
    loadRunConfiguration in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getOutput

    +
    +public java.lang.String getOutput()
    +
    +
    +
    Specified by:
    getOutput in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getError

    +
    +public java.lang.String getError()
    +
    +
    +
    Specified by:
    getError in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<NetNglyc> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<NetNglyc> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<NetNglyc>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/OB.html b/website/full_javadoc/compbio/runner/_impl/OB.html new file mode 100644 index 0000000..55d1730 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/OB.html @@ -0,0 +1,382 @@ + + + + + + +OB + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class OB

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.OB
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class OB
    extends _SkeletalCommandBuilder
    + + +

    +TODO this needs fixing! Executable does not work +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + + + + +
    +Constructor Summary
    OB() + +
    +           
    OB(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + java.util.List<java.lang.String>getTestArgs() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +OB

    +
    +public OB()
    +
    +
    +
    + +

    +OB

    +
    +public OB(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getTestArgs

    +
    +public java.util.List<java.lang.String> getTestArgs()
    +
    +
    +
    +
    +
    +
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html new file mode 100644 index 0000000..b14bdb4 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/PSIBlast.html @@ -0,0 +1,360 @@ + + + + + + +PSIBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class PSIBlast

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.PSIBlast
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class PSIBlast
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    PSIBlast(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    + booleanremoveOutput(java.lang.String outfile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PSIBlast

    +
    +public PSIBlast(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +removeOutput

    +
    +public boolean removeOutput(java.lang.String outfile)
    +
    +
    +
    +
    +
    +
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html new file mode 100644 index 0000000..64cecfd --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/RPSBlast.html @@ -0,0 +1,360 @@ + + + + + + +RPSBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class RPSBlast

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.RPSBlast
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class RPSBlast
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    RPSBlast(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    +static java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +RPSBlast

    +
    +public RPSBlast(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public static java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/Ronn.html b/website/full_javadoc/compbio/runner/_impl/Ronn.html new file mode 100644 index 0000000..d5f9998 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Ronn.html @@ -0,0 +1,360 @@ + + + + + + +Ronn + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class Ronn

    +
    +java.lang.Object
+  extended by compbio.runner._SkeletalCommandBuilder
+      extended by compbio.runner._impl.Ronn
+
    +
    +
    All Implemented Interfaces:
    Executable<_SkeletalCommandBuilder>
    +
    +
    +
    +
    public class Ronn
    extends _SkeletalCommandBuilder
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    Ronn(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.StringgetCommand(Executable.ExecProvider provider) + +
    +           
    + java.lang.StringgetCommandName() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +           
    + java.lang.StringgetInput() + +
    +           
    +static java.lang.StringgetTestCommand() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.runner._SkeletalCommandBuilder
    addParameter, addParameters, addParameters, getEmail, getError, getLimit, getLimits, getName, getOutput, getParameters, getResults, loadRunConfiguration, setEmail, setName
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +Ronn

    +
    +public Ronn(java.lang.String workDirectory)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getCommand

    +
    +public java.lang.String getCommand(Executable.ExecProvider provider)
    +
    +
    +
    +
    +
    +
    + +

    +getTestCommand

    +
    +public static java.lang.String getTestCommand()
    +
    +
    +
    +
    +
    +
    + +

    +getCommandName

    +
    +public java.lang.String getCommandName()
    +
    +
    +
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    +
    +
    +
    +
    + +

    +getInput

    +
    +public java.lang.String getInput()
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/Runners.html b/website/full_javadoc/compbio/runner/_impl/Runners.html new file mode 100644 index 0000000..3a3978d --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/Runners.html @@ -0,0 +1,371 @@ + + + + + + +Runners + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._impl +
    +Class Runners

    +
    +java.lang.Object
+  extended by compbio.runner._impl.Runners
+
    +
    +
    +
    public final class Runners
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static BlastAllgetBlastAllRunnable(java.lang.String workDirectory) + +
    +           
    +static DisemblgetDisemblRunnable(java.lang.String workDirectory) + +
    +           
    +static MclgetMclRunnable(java.lang.String workDirectory) + +
    +           
    +static NetNglycgetNetNglycRunnable(java.lang.String workDirectory) + +
    +           
    +static OBgetOBRunnable(java.lang.String workDirectory) + +
    +           
    +static PSIBlastgetPSIBlastRunnable(java.lang.String workDirectory) + +
    +           
    +static RonngetRonnRunnable(java.lang.String workDirectory) + +
    +           
    +static RPSBlastgetRPSBlastRunnable(java.lang.String workDirectory) + +
    +           
    +static compbio.runner._impl.Tmhmm2getTmhmm2Runnable(java.lang.String workDirectory) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +getMclRunnable

    +
    +public static Mcl getMclRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getOBRunnable

    +
    +public static OB getOBRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getDisemblRunnable

    +
    +public static Disembl getDisemblRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getNetNglycRunnable

    +
    +public static NetNglyc getNetNglycRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getRonnRunnable

    +
    +public static Ronn getRonnRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getTmhmm2Runnable

    +
    +public static compbio.runner._impl.Tmhmm2 getTmhmm2Runnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getRPSBlastRunnable

    +
    +public static RPSBlast getRPSBlastRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getBlastAllRunnable

    +
    +public static BlastAll getBlastAllRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    +
    + +

    +getPSIBlastRunnable

    +
    +public static PSIBlast getPSIBlastRunnable(java.lang.String workDirectory)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html new file mode 100644 index 0000000..6389cd6 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/BlastAll.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.BlastAll + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.BlastAll

    +
    + + + + + + + + + +
    +Packages that use BlastAll
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of BlastAll in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return BlastAll
    +static BlastAllRunners.getBlastAllRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html new file mode 100644 index 0000000..8ebcce6 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/BlastParameters.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.BlastParameters + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.BlastParameters

    +
    +No usage of compbio.runner._impl.BlastParameters +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html new file mode 100644 index 0000000..005572a --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Disembl.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Disembl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.Disembl

    +
    + + + + + + + + + +
    +Packages that use Disembl
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of Disembl in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Disembl
    +static DisemblRunners.getDisemblRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html b/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html new file mode 100644 index 0000000..243aeae --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Environment.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.Environment + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +    		 + +
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    +

    +Uses of Class
    compbio.runner._impl.Environment

    +
    +No usage of compbio.runner._impl.Environment +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html new file mode 100644 index 0000000..d08bb98 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Mcl.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Mcl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    +

    +Uses of Class
    compbio.runner._impl.Mcl

    +
    + + + + + + + + + +
    +Packages that use Mcl
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of Mcl in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Mcl
    +static MclRunners.getMclRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html new file mode 100644 index 0000000..ecd9ab5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/NetNglyc.html @@ -0,0 +1,220 @@ + + + + + + +Uses of Class compbio.runner._impl.NetNglyc + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.NetNglyc

    +
    + + + + + + + + + +
    +Packages that use NetNglyc
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of NetNglyc in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner._impl that return NetNglyc
    + NetNglycNetNglyc.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    +static NetNglycRunners.getNetNglycRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner._impl that return types with arguments of type NetNglyc
    + Limit<NetNglyc>NetNglyc.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<NetNglyc>NetNglyc.getLimits() + +
    +           
    + CommandBuilder<NetNglyc>NetNglyc.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/OB.html b/website/full_javadoc/compbio/runner/_impl/class-use/OB.html new file mode 100644 index 0000000..ce2519a --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/OB.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.OB + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.OB

    +
    + + + + + + + + + +
    +Packages that use OB
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of OB in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return OB
    +static OBRunners.getOBRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html new file mode 100644 index 0000000..8bc9956 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/PSIBlast.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.PSIBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.PSIBlast

    +
    + + + + + + + + + +
    +Packages that use PSIBlast
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of PSIBlast in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return PSIBlast
    +static PSIBlastRunners.getPSIBlastRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html new file mode 100644 index 0000000..a1f52e3 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/RPSBlast.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.RPSBlast + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._impl.RPSBlast

    +
    + + + + + + + + + +
    +Packages that use RPSBlast
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of RPSBlast in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return RPSBlast
    +static RPSBlastRunners.getRPSBlastRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html new file mode 100644 index 0000000..cc6975e --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Ronn.html @@ -0,0 +1,180 @@ + + + + + + +Uses of Class compbio.runner._impl.Ronn + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.Ronn

    +
    + + + + + + + + + +
    +Packages that use Ronn
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of Ronn in compbio.runner._impl
    +  +

    + + + + + + + + + +
    Methods in compbio.runner._impl that return Ronn
    +static RonnRunners.getRonnRunnable(java.lang.String workDirectory) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html b/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html new file mode 100644 index 0000000..af87076 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/class-use/Runners.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._impl.Runners + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.runner._impl.Runners

    +
    +No usage of compbio.runner._impl.Runners +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-frame.html b/website/full_javadoc/compbio/runner/_impl/package-frame.html new file mode 100644 index 0000000..55be9ff --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-frame.html @@ -0,0 +1,52 @@ + + + + + + +compbio.runner._impl + + + + + + + + + + + +compbio.runner._impl + + + + +
    +Classes  + +
    +BlastAll +
    +BlastParameters +
    +Disembl +
    +Environment +
    +Mcl +
    +NetNglyc +
    +OB +
    +PSIBlast +
    +Ronn +
    +RPSBlast +
    +Runners
    + + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-summary.html b/website/full_javadoc/compbio/runner/_impl/package-summary.html new file mode 100644 index 0000000..c985bf0 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-summary.html @@ -0,0 +1,197 @@ + + + + + + +compbio.runner._impl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.runner._impl +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    BlastAll 
    BlastParametersUtility class for common Blast parameters
    Disembl 
    EnvironmentThis is utility class to encapsulate environmental variables like directory paths
    Mcl 
    NetNglyc 
    OBTODO this needs fixing! Executable does not work
    PSIBlast 
    Ronn 
    RPSBlast 
    Runners 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-tree.html b/website/full_javadoc/compbio/runner/_impl/package-tree.html new file mode 100644 index 0000000..3f894d8 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-tree.html @@ -0,0 +1,157 @@ + + + + + + +compbio.runner._impl Class Hierarchy + + + + + + + + + + + + +
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    + + + + + + + + + + + + +
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    +    		 + +
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    +

    +Hierarchy For Package compbio.runner._impl +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    + +
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    +    		 + +
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    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_impl/package-use.html b/website/full_javadoc/compbio/runner/_impl/package-use.html new file mode 100644 index 0000000..5ada742 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_impl/package-use.html @@ -0,0 +1,212 @@ + + + + + + +Uses of Package compbio.runner._impl + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Package
    compbio.runner._impl

    +
    + + + + + + + + + +
    +Packages that use compbio.runner._impl
    compbio.runner._impl  
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner._impl used by compbio.runner._impl
    BlastAll + +
    +           
    Disembl + +
    +           
    Mcl + +
    +           
    NetNglyc + +
    +           
    OB + +
    +          TODO this needs fixing! Executable does not work
    PSIBlast + +
    +           
    Ronn + +
    +           
    RPSBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/_Jpred.html new file mode 100644 index 0000000..4eee1a7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/_Jpred.html @@ -0,0 +1,224 @@ + + + + + + +_Jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner._jpred +
    +Class _Jpred

    +
    +java.lang.Object
+  extended by compbio.runner._jpred._Jpred
+
    +
    +
    +
    public class _Jpred
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    _Jpred() + +
    +           
    +  + + + + + + + +
    +Method Summary
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +_Jpred

    +
    +public _Jpred()
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html b/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html new file mode 100644 index 0000000..fd98536 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/class-use/_Jpred.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._jpred._Jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._jpred._Jpred

    +
    +No usage of compbio.runner._jpred._Jpred +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-frame.html b/website/full_javadoc/compbio/runner/_jpred/package-frame.html new file mode 100644 index 0000000..2640f34 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-frame.html @@ -0,0 +1,32 @@ + + + + + + +compbio.runner._jpred + + + + + + + + + + + +compbio.runner._jpred + + + + +
    +Classes  + +
    +_Jpred
    + + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-summary.html b/website/full_javadoc/compbio/runner/_jpred/package-summary.html new file mode 100644 index 0000000..f375d9f --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-summary.html @@ -0,0 +1,157 @@ + + + + + + +compbio.runner._jpred + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +

    +Package compbio.runner._jpred +

    + + + + + + + + + +
    +Class Summary
    _Jpred 
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview   Package  Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV PACKAGE  + NEXT PACKAGE + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-tree.html b/website/full_javadoc/compbio/runner/_jpred/package-tree.html new file mode 100644 index 0000000..e9e4095 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-tree.html @@ -0,0 +1,153 @@ + + + + + + +compbio.runner._jpred Class Hierarchy + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    +

    +Hierarchy For Package compbio.runner._jpred +

    +
    +
    +
    Package Hierarchies:
    All Packages
    +
    +

    +Class Hierarchy +

    +
      +
    • java.lang.Object
        +
      • compbio.runner._jpred._Jpred
      +
    +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/_jpred/package-use.html b/website/full_javadoc/compbio/runner/_jpred/package-use.html new file mode 100644 index 0000000..dd3eac5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/_jpred/package-use.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Package compbio.runner._jpred + + + + + + + + + + + + +
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    +Uses of Package
    compbio.runner._jpred

    +
    +No usage of compbio.runner._jpred +

    +

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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html b/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html new file mode 100644 index 0000000..82f1f31 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/OptionCombinator.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner.OptionCombinator + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Uses of Class
    compbio.runner.OptionCombinator

    +
    +No usage of compbio.runner.OptionCombinator +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/Util.html b/website/full_javadoc/compbio/runner/class-use/Util.html new file mode 100644 index 0000000..7d1eef5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/Util.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner.Util + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
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    +Uses of Class
    compbio.runner.Util

    +
    +No usage of compbio.runner.Util +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html b/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html new file mode 100644 index 0000000..cbcc70d --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/_NativeSpecHelper.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.runner._NativeSpecHelper + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner._NativeSpecHelper

    +
    +No usage of compbio.runner._NativeSpecHelper +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html b/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html new file mode 100644 index 0000000..46aa6c4 --- /dev/null +++ b/website/full_javadoc/compbio/runner/class-use/_SkeletalCommandBuilder.html @@ -0,0 +1,321 @@ + + + + + + +Uses of Class compbio.runner._SkeletalCommandBuilder + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
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    +
    +

    +Uses of Class
    compbio.runner._SkeletalCommandBuilder

    +
    + + + + + + + + + + + + + +
    +Packages that use _SkeletalCommandBuilder
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    +  +

    + + + + + +
    +Uses of _SkeletalCommandBuilder in compbio.runner
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner that return _SkeletalCommandBuilder
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameter(java.lang.String parameter) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.util.List<java.lang.String> parameters) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.addParameters(java.lang.String[] parameters) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.setEmail(java.lang.String email) + +
    +           
    + _SkeletalCommandBuilder_SkeletalCommandBuilder.setName(java.lang.String name) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner that return types with arguments of type _SkeletalCommandBuilder
    + Limit<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getLimits() + +
    +           
    + CommandBuilder<_SkeletalCommandBuilder>_SkeletalCommandBuilder.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of _SkeletalCommandBuilder in compbio.runner._impl
    +  +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Subclasses of _SkeletalCommandBuilder in compbio.runner._impl
    + classBlastAll + +
    +           
    + classDisembl + +
    +           
    + classMcl + +
    +           
    + classOB + +
    +          TODO this needs fixing! Executable does not work
    + classPSIBlast + +
    +           
    + classRonn + +
    +           
    + classRPSBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/ClustalW.html b/website/full_javadoc/compbio/runner/msa/ClustalW.html new file mode 100644 index 0000000..e2cbdb5 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/ClustalW.html @@ -0,0 +1,473 @@ + + + + + + +ClustalW + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.msa +
    +Class ClustalW

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<ClustalW>
+      extended by compbio.runner.msa.ClustalW
+
    +
    +
    All Implemented Interfaces:
    Executable<ClustalW>
    +
    +
    +
    +
    public class ClustalW
    extends SkeletalExecutable<ClustalW>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    ClustalW() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<ClustalW>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<ClustalW>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    +static java.lang.StringgetStatFile() + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + ClustalWsetInput(java.lang.String inFile) + +
    +           
    + ClustalWsetOutput(java.lang.String outFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +KEY_VALUE_SEPARATOR

    +
    +public static final java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +ClustalW

    +
    +public ClustalW()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setOutput

    +
    +public ClustalW setOutput(java.lang.String outFile)
    +
    +
    +
    Overrides:
    setOutput in class SkeletalExecutable<ClustalW>
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public ClustalW setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<ClustalW>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    Description copied from class: SkeletalExecutable
    +
    This method cannot really tell whether the files has actually been + created or not. It must be overridden as required. +

    +

    +
    Specified by:
    getCreatedFiles in interface Executable<ClustalW>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<ClustalW>
    +
    +
    +
    See Also:
    Executable.getCreatedFiles()
    +
    +
    +
    + +

    +getStatFile

    +
    +public static java.lang.String getStatFile()
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<ClustalW> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<ClustalW> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<ClustalW>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Mafft.html b/website/full_javadoc/compbio/runner/msa/Mafft.html new file mode 100644 index 0000000..0a6d12c --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Mafft.html @@ -0,0 +1,448 @@ + + + + + + +Mafft + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.msa +
    +Class Mafft

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<Mafft>
+      extended by compbio.runner.msa.Mafft
+
    +
    +
    All Implemented Interfaces:
    Executable<Mafft>, PipedExecutable<Mafft>
    +
    +
    +
    +
    public class Mafft
    extends SkeletalExecutable<Mafft>
    implements PipedExecutable<Mafft>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Mafft() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + MafftaddParameters(java.util.List<java.lang.String> parameters) + +
    +          Mafft input must always be the last parameter!
    + Limit<Mafft>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Mafft>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + MafftsetInput(java.lang.String inFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    equals, getClusterSettings, getCreatedFiles, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    getCreatedFiles, getError, getInput, getOutput, getParameters, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +KEY_VALUE_SEPARATOR

    +
    +public static final java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Mafft

    +
    +public Mafft()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Mafft>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +setInput

    +
    +public Mafft setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +addParameters

    +
    +public Mafft addParameters(java.util.List<java.lang.String> parameters)
    +
    +
    Mafft input must always be the last parameter! +

    +

    +
    Specified by:
    addParameters in interface Executable<Mafft>
    Overrides:
    addParameters in class SkeletalExecutable<Mafft>
    +
    +
    + +
    Returns:
    this Executable
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Mafft> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Mafft> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Mafft>
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Mafft>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Muscle.html b/website/full_javadoc/compbio/runner/msa/Muscle.html new file mode 100644 index 0000000..479eb57 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Muscle.html @@ -0,0 +1,481 @@ + + + + + + +Muscle + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.msa +
    +Class Muscle

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<Muscle>
+      extended by compbio.runner.msa.Muscle
+
    +
    +
    All Implemented Interfaces:
    Executable<Muscle>
    +
    +
    +
    +
    public class Muscle
    extends SkeletalExecutable<Muscle>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Muscle() + +
    +          Default options are + + -clwstrict - write output in clustal format
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Muscle>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Muscle>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    +static java.lang.StringgetStatFile() + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + MusclesetInput(java.lang.String inFile) + +
    +           
    + MusclesetOutput(java.lang.String outFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +KEY_VALUE_SEPARATOR

    +
    +public static final java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Muscle

    +
    +public Muscle()
    +
    +
    Default options are + + -clwstrict - write output in clustal format +

    +

    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setOutput

    +
    +public Muscle setOutput(java.lang.String outFile)
    +
    +
    +
    Overrides:
    setOutput in class SkeletalExecutable<Muscle>
    +
    +
    +
    +
    +
    +
    + +

    +setInput

    +
    +public Muscle setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Muscle>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    Description copied from class: SkeletalExecutable
    +
    This method cannot really tell whether the files has actually been + created or not. It must be overridden as required. +

    +

    +
    Specified by:
    getCreatedFiles in interface Executable<Muscle>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Muscle>
    +
    +
    +
    See Also:
    Executable.getCreatedFiles()
    +
    +
    +
    + +

    +getStatFile

    +
    +public static java.lang.String getStatFile()
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Muscle> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Muscle> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Muscle>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Probcons.html b/website/full_javadoc/compbio/runner/msa/Probcons.html new file mode 100644 index 0000000..74a2d6a --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Probcons.html @@ -0,0 +1,452 @@ + + + + + + +Probcons + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.msa +
    +Class Probcons

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<Probcons>
+      extended by compbio.runner.msa.Probcons
+
    +
    +
    All Implemented Interfaces:
    Executable<Probcons>, PipedExecutable<Probcons>
    +
    +
    +
    +
    public class Probcons
    extends SkeletalExecutable<Probcons>
    implements PipedExecutable<Probcons>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Probcons() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Probcons>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Probcons>getLimits() + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + ProbconssetInput(java.lang.String inFile) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getError, getInput, getOutput, getParameters, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +KEY_VALUE_SEPARATOR

    +
    +public static final java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Probcons

    +
    +public Probcons()
    +
    +
    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Probcons>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    Description copied from class: SkeletalExecutable
    +
    This method cannot really tell whether the files has actually been + created or not. It must be overridden as required. +

    +

    +
    Specified by:
    getCreatedFiles in interface Executable<Probcons>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Probcons>
    +
    +
    +
    See Also:
    Executable.getCreatedFiles()
    +
    +
    +
    + +

    +setInput

    +
    +public Probcons setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Probcons> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Probcons> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Probcons>
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Probcons>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/Tcoffee.html new file mode 100644 index 0000000..b35bcc1 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/Tcoffee.html @@ -0,0 +1,542 @@ + + + + + + +Tcoffee + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.msa +
    +Class Tcoffee

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<Tcoffee>
+      extended by compbio.runner.msa.Tcoffee
+
    +
    +
    All Implemented Interfaces:
    ClusterNativeSpecExecutable<Tcoffee>, Executable<Tcoffee>, PipedExecutable<Tcoffee>
    +
    +
    +
    +
    public class Tcoffee
    extends SkeletalExecutable<Tcoffee>
    implements PipedExecutable<Tcoffee>, ClusterNativeSpecExecutable<Tcoffee>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Field Summary
    +static java.lang.StringKEY_VALUE_SEPARATOR + +
    +           
    +  + + + + + + + + + + +
    +Constructor Summary
    Tcoffee() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static intgetClusterCpuNum() + +
    +           
    + java.util.List<java.lang.String>getCreatedFiles() + +
    +          This method cannot really tell whether the files has actually been + created or not.
    + Limit<Tcoffee>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Tcoffee>getLimits() + +
    +           
    + java.lang.StringgetNativeSpecs() + +
    +           
    + CommandBuilder<Tcoffee>getParameters(Executable.ExecProvider provider) + +
    +           
    + AlignmentgetResults(java.lang.String workDirectory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    + TcoffeesetInput(java.lang.String inFile) + +
    +           
    + voidsetNCore(int ncoreNumber) + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getError, getInput, getOutput, hashCode, loadRunConfiguration, setError, setOutput, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  + + + + + + + +
    Methods inherited from interface compbio.engine.client.Executable
    addParameters, getError, getInput, getOutput, loadRunConfiguration
    +  +

    + + + + + + + + +
    +Field Detail
    + +

    +KEY_VALUE_SEPARATOR

    +
    +public static final java.lang.String KEY_VALUE_SEPARATOR
    +
    +
    +
    See Also:
    Constant Field Values
    +
    + + + + + + + + +
    +Constructor Detail
    + +

    +Tcoffee

    +
    +public Tcoffee()
    +
    +
    +
    Parameters:
    workDirectory -
    +
    + + + + + + + + +
    +Method Detail
    + +

    +setInput

    +
    +public Tcoffee setInput(java.lang.String inFile)
    +
    +
    +
    Overrides:
    setInput in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getResults

    +
    +public Alignment getResults(java.lang.String workDirectory)
+                     throws ResultNotAvailableException
    +
    +
    +
    Specified by:
    getResults in interface Executable<Tcoffee>
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getCreatedFiles

    +
    +public java.util.List<java.lang.String> getCreatedFiles()
    +
    +
    Description copied from class: SkeletalExecutable
    +
    This method cannot really tell whether the files has actually been + created or not. It must be overridden as required. +

    +

    +
    Specified by:
    getCreatedFiles in interface Executable<Tcoffee>
    Overrides:
    getCreatedFiles in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    See Also:
    Executable.getCreatedFiles()
    +
    +
    +
    + +

    +setNCore

    +
    +public void setNCore(int ncoreNumber)
    +
    +
    +
    +
    +
    +
    +
    +
    +
    + +

    +getParameters

    +
    +public CommandBuilder<Tcoffee> getParameters(Executable.ExecProvider provider)
    +
    +
    +
    Specified by:
    getParameters in interface Executable<Tcoffee>
    Overrides:
    getParameters in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Tcoffee> getLimit(java.lang.String presetName)
    +
    +
    +
    Specified by:
    getLimit in interface Executable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Tcoffee> getLimits()
    +
    +
    +
    Specified by:
    getLimits in interface Executable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getNativeSpecs

    +
    +public java.lang.String getNativeSpecs()
    +
    +
    +
    Specified by:
    getNativeSpecs in interface ClusterNativeSpecExecutable<Tcoffee>
    +
    +
    +
    +
    +
    +
    + +

    +getClusterCpuNum

    +
    +public static int getClusterCpuNum()
    +
    +
    +
    +
    +
    + +
    Returns:
    number of cpus to use on the cluster or 0 if the value is + undefined
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<Tcoffee>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html new file mode 100644 index 0000000..5d5eecf --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/ClustalW.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.ClustalW + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner.msa.ClustalW

    +
    + + + + + + + + + + + + + +
    +Packages that use ClustalW
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of ClustalW in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return ClustalW
    + ClustalWClustalW.setInput(java.lang.String inFile) + +
    +           
    + ClustalWClustalW.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type ClustalW
    + Limit<ClustalW>ClustalW.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<ClustalW>ClustalW.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of ClustalW in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type ClustalW
    + Limit<ClustalW>ClustalWS.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<ClustalW>ClustalWS.getLimits() + +
    +           
    + PresetManager<ClustalW>ClustalWS.getPresets() + +
    +           
    + RunnerConfig<ClustalW>ClustalWS.getRunnerOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type ClustalW
    + java.lang.StringClustalWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +           
    + java.lang.StringClustalWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html new file mode 100644 index 0000000..65e6512 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Mafft.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.Mafft + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner.msa.Mafft

    +
    + + + + + + + + + + + + + +
    +Packages that use Mafft
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Mafft in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Mafft
    + MafftMafft.addParameters(java.util.List<java.lang.String> parameters) + +
    +          Mafft input must always be the last parameter!
    + MafftMafft.setInput(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Mafft
    + Limit<Mafft>Mafft.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Mafft>Mafft.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Mafft in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Mafft
    + Limit<Mafft>MafftWS.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Mafft>MafftWS.getLimits() + +
    +           
    + PresetManager<Mafft>MafftWS.getPresets() + +
    +           
    + RunnerConfig<Mafft>MafftWS.getRunnerOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Mafft
    + java.lang.StringMafftWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +           
    + java.lang.StringMafftWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html new file mode 100644 index 0000000..2621067 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Muscle.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.Muscle + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.runner.msa.Muscle

    +
    + + + + + + + + + + + + + +
    +Packages that use Muscle
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Muscle in compbio.runner.msa
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return Muscle
    + MuscleMuscle.setInput(java.lang.String inFile) + +
    +           
    + MuscleMuscle.setOutput(java.lang.String outFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Muscle
    + Limit<Muscle>Muscle.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Muscle>Muscle.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Muscle in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Muscle
    + Limit<Muscle>MuscleWS.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Muscle>MuscleWS.getLimits() + +
    +           
    + PresetManager<Muscle>MuscleWS.getPresets() + +
    +           
    + RunnerConfig<Muscle>MuscleWS.getRunnerOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Muscle
    + java.lang.StringMuscleWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +           
    + java.lang.StringMuscleWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html new file mode 100644 index 0000000..3ffa0e0 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Probcons.html @@ -0,0 +1,283 @@ + + + + + + +Uses of Class compbio.runner.msa.Probcons + + + + + + + + + + + + +
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    +Uses of Class
    compbio.runner.msa.Probcons

    +
    + + + + + + + + + + + + + +
    +Packages that use Probcons
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Probcons in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.msa that return Probcons
    + ProbconsProbcons.setInput(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Probcons
    + Limit<Probcons>Probcons.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Probcons>Probcons.getLimits() + +
    +           
    +  +

    + + + + + +
    +Uses of Probcons in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Probcons
    + Limit<Probcons>ProbconsWS.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Probcons>ProbconsWS.getLimits() + +
    +           
    + PresetManager<Probcons>ProbconsWS.getPresets() + +
    +           
    + RunnerConfig<Probcons>ProbconsWS.getRunnerOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Probcons
    + java.lang.StringProbconsWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +           
    + java.lang.StringProbconsWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html new file mode 100644 index 0000000..243fcd9 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/class-use/Tcoffee.html @@ -0,0 +1,291 @@ + + + + + + +Uses of Class compbio.runner.msa.Tcoffee + + + + + + + + + + + + +
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    +Uses of Class
    compbio.runner.msa.Tcoffee

    +
    + + + + + + + + + + + + + +
    +Packages that use Tcoffee
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + +
    +Uses of Tcoffee in compbio.runner.msa
    +  +

    + + + + + + + + + +
    Methods in compbio.runner.msa that return Tcoffee
    + TcoffeeTcoffee.setInput(java.lang.String inFile) + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + +
    Methods in compbio.runner.msa that return types with arguments of type Tcoffee
    + Limit<Tcoffee>Tcoffee.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Tcoffee>Tcoffee.getLimits() + +
    +           
    + CommandBuilder<Tcoffee>Tcoffee.getParameters(Executable.ExecProvider provider) + +
    +           
    +  +

    + + + + + +
    +Uses of Tcoffee in compbio.ws.server
    +  +

    + + + + + + + + + + + + + + + + + + + + + +
    Methods in compbio.ws.server that return types with arguments of type Tcoffee
    + Limit<Tcoffee>TcoffeeWS.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<Tcoffee>TcoffeeWS.getLimits() + +
    +           
    + PresetManager<Tcoffee>TcoffeeWS.getPresets() + +
    +           
    + RunnerConfig<Tcoffee>TcoffeeWS.getRunnerOptions() + +
    +           
    +  +

    + + + + + + + + + + + + + +
    Method parameters in compbio.ws.server with type arguments of type Tcoffee
    + java.lang.StringTcoffeeWS.customAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +           
    + java.lang.StringTcoffeeWS.presetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +           
    +  +

    +

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    +Classes  + +
    +ClustalW +
    +Mafft +
    +Muscle +
    +Probcons +
    +Tcoffee
    + + + + diff --git a/website/full_javadoc/compbio/runner/msa/package-summary.html b/website/full_javadoc/compbio/runner/msa/package-summary.html new file mode 100644 index 0000000..82e1c12 --- /dev/null +++ b/website/full_javadoc/compbio/runner/msa/package-summary.html @@ -0,0 +1,192 @@ + + + + + + +compbio.runner.msa + + + + + + + + + + + + +
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    +

    +Package compbio.runner.msa +

    +Wrappers for native executables for multiple sequence alignment (msa) +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    ClustalW 
    Mafft 
    Muscle 
    Probcons 
    Tcoffee 
    +  + +

    +

    +Package compbio.runner.msa Description +

    + +

    +Wrappers for native executables for multiple sequence alignment (msa) +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
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    +Hierarchy For Package compbio.runner.msa +

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    +
    +

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    +Uses of Package
    compbio.runner.msa

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.runner.msa
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa) 
    compbio.ws.server  
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner.msa used by compbio.runner.msa
    ClustalW + +
    +           
    Mafft + +
    +           
    Muscle + +
    +           
    Probcons + +
    +           
    Tcoffee + +
    +           
    +  +

    + + + + + + + + + + + + + + + + + + + + +
    +Classes in compbio.runner.msa used by compbio.ws.server
    ClustalW + +
    +           
    Mafft + +
    +           
    Muscle + +
    +           
    Probcons + +
    +           
    Tcoffee + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/package-frame.html b/website/full_javadoc/compbio/runner/package-frame.html new file mode 100644 index 0000000..6fd25a9 --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-frame.html @@ -0,0 +1,38 @@ + + + + + + +compbio.runner + + + + + + + + + + + +compbio.runner + + + + +
    +Classes  + +
    +_NativeSpecHelper +
    +_SkeletalCommandBuilder +
    +OptionCombinator +
    +Util
    + + + + diff --git a/website/full_javadoc/compbio/runner/package-summary.html b/website/full_javadoc/compbio/runner/package-summary.html new file mode 100644 index 0000000..e5f3a22 --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-summary.html @@ -0,0 +1,188 @@ + + + + + + +compbio.runner + + + + + + + + + + + + +
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    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +

    +Package compbio.runner +

    +Utilities commonly used by all runners. +

    +See: +
    +          Description +

    + + + + + + + + + + + + + + + + + + + + + +
    +Class Summary
    _NativeSpecHelper 
    _SkeletalCommandBuilder 
    OptionCombinatorThis class solve the following problems.
    Util 
    +  + +

    +

    +Package compbio.runner Description +

    + +

    +Utilities commonly used by all runners. +

    + +

    +

    +
    Author:
    +
    Petr Troshin + + Date January 2010
    +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/runner/package-tree.html b/website/full_javadoc/compbio/runner/package-tree.html new file mode 100644 index 0000000..05b744b --- /dev/null +++ b/website/full_javadoc/compbio/runner/package-tree.html @@ -0,0 +1,154 @@ + + + + + + +compbio.runner Class Hierarchy + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.runner +

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    +
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    +Uses of Package
    compbio.runner

    +
    + + + + + + + + + + + + + +
    +Packages that use compbio.runner
    compbio.runnerUtilities commonly used by all runners. 
    compbio.runner._impl  
    +  +

    + + + + + + + + +
    +Classes in compbio.runner used by compbio.runner
    _SkeletalCommandBuilder + +
    +           
    +  +

    + + + + + + + + +
    +Classes in compbio.runner used by compbio.runner._impl
    _SkeletalCommandBuilder + +
    +           
    +  +

    +

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    + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html b/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html new file mode 100644 index 0000000..072dda7 --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/PsiBlast.html @@ -0,0 +1,354 @@ + + + + + + +PsiBlast + + + + + + + + + + + + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.runner.psiblast +
    +Class PsiBlast

    +
    +java.lang.Object
+  extended by compbio.engine.client.SkeletalExecutable<PsiBlast>
+      extended by compbio.runner.psiblast.PsiBlast
+
    +
    +
    All Implemented Interfaces:
    Executable<PsiBlast>
    +
    +
    +
    +
    public class PsiBlast
    extends SkeletalExecutable<PsiBlast>
    + + +

    +

    + +

    + + + + + + + +
    +Nested Class Summary
    +  + + + + + + + +
    Nested classes/interfaces inherited from interface compbio.engine.client.Executable
    Executable.ExecProvider
    +  + + + + + + + + + + + +
    +Constructor Summary
    PsiBlast() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + Limit<PsiBlast>getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<PsiBlast>getLimits() + +
    +           
    + + + + + +
    +<V> V
    +    		getResults(java.lang.String directory) + +
    +           
    + java.lang.Class<? extends Executable<?>>getType() + +
    +           
    +  + + + + + + + +
    Methods inherited from class compbio.engine.client.SkeletalExecutable
    addParameters, equals, getClusterSettings, getCreatedFiles, getError, getInput, getOutput, getParameters, hashCode, loadRunConfiguration, setError, setInput, setOutput, setParameter, toString
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +PsiBlast

    +
    +public PsiBlast()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +getResults

    +
    +public <V> V getResults(java.lang.String directory)
+             throws ResultNotAvailableException
    +
    +
    + +
    Throws: +
    ResultNotAvailableException
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<PsiBlast> getLimit(java.lang.String presetName)
    +
    +
    +
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<PsiBlast> getLimits()
    +
    +
    +
    +
    +
    +
    + +

    +getType

    +
    +public java.lang.Class<? extends Executable<?>> getType()
    +
    +
    +
    Specified by:
    getType in class SkeletalExecutable<PsiBlast>
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html b/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html new file mode 100644 index 0000000..278d08b --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/class-use/PsiBlast.html @@ -0,0 +1,188 @@ + + + + + + +Uses of Class compbio.runner.psiblast.PsiBlast + + + + + + + + + + + + +
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    + + + + + + + + + + + + +
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    +

    +Uses of Class
    compbio.runner.psiblast.PsiBlast

    +
    + + + + + + + + + +
    +Packages that use PsiBlast
    compbio.runner.psiblast  
    +  +

    + + + + + +
    +Uses of PsiBlast in compbio.runner.psiblast
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.runner.psiblast that return types with arguments of type PsiBlast
    + Limit<PsiBlast>PsiBlast.getLimit(java.lang.String presetName) + +
    +           
    + LimitsManager<PsiBlast>PsiBlast.getLimits() + +
    +           
    +  +

    +

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    + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/package-frame.html b/website/full_javadoc/compbio/runner/psiblast/package-frame.html new file mode 100644 index 0000000..0397a2b --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/package-frame.html @@ -0,0 +1,32 @@ + + + + + + +compbio.runner.psiblast + + + + + + + + + + + +compbio.runner.psiblast + + + + +
    +Classes  + +
    +PsiBlast
    + + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/package-summary.html b/website/full_javadoc/compbio/runner/psiblast/package-summary.html new file mode 100644 index 0000000..869c38b --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/package-summary.html @@ -0,0 +1,157 @@ + + + + + + +compbio.runner.psiblast + + + + + + + + + + + + +
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    +Package compbio.runner.psiblast +

    + + + + + + + + + +
    +Class Summary
    PsiBlast 
    +  + +

    +

    +
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    + + + diff --git a/website/full_javadoc/compbio/runner/psiblast/package-tree.html b/website/full_javadoc/compbio/runner/psiblast/package-tree.html new file mode 100644 index 0000000..3af50a4 --- /dev/null +++ b/website/full_javadoc/compbio/runner/psiblast/package-tree.html @@ -0,0 +1,156 @@ + + + + + + +compbio.runner.psiblast Class Hierarchy + + + + + + + + + + + + +
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    + + + + + + + + + + + + +
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    Package Hierarchies:
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    +
    +

    +Class Hierarchy +

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    +Uses of Package
    compbio.runner.psiblast

    +
    + + + + + + + + + +
    +Packages that use compbio.runner.psiblast
    compbio.runner.psiblast  
    +  +

    + + + + + + + + +
    +Classes in compbio.runner.psiblast used by compbio.runner.psiblast
    PsiBlast + +
    +           
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html new file mode 100644 index 0000000..35584df --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/Jws2Client.Services.html @@ -0,0 +1,377 @@ + + + + + + +Jws2Client.Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Enum Jws2Client.Services

    +
    +java.lang.Object
+  extended by java.lang.Enum<Jws2Client.Services>
+      extended by compbio.ws.client.Jws2Client.Services
+
    +
    +
    All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<Jws2Client.Services>
    +
    +
    +
    Enclosing class:
    Jws2Client
    +
    +
    +
    +
    public static enum Jws2Client.Services
    extends java.lang.Enum<Jws2Client.Services>
    + + +

    +List of web services currently supported by JWS2 +

    + +

    +

    + +

    + + + + + + + + + + + + + + + + + + + + + + +
    +Enum Constant Summary
    ClustalWS + +
    +           
    MafftWS + +
    +           
    MuscleWS + +
    +           
    ProbconsWS + +
    +           
    TcoffeeWS + +
    +           
    +  + + + + + + + + + + + + + + + +
    +Method Summary
    +static Jws2Client.ServicesvalueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Jws2Client.Services[]values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  + + + + + + + +
    Methods inherited from class java.lang.Enum
    compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    getClass, notify, notifyAll, wait, wait, wait
    +  +

    + + + + + + + + +
    +Enum Constant Detail
    + +

    +MafftWS

    +
    +public static final Jws2Client.Services MafftWS
    +
    +
    +
    +
    +
    + +

    +MuscleWS

    +
    +public static final Jws2Client.Services MuscleWS
    +
    +
    +
    +
    +
    + +

    +ClustalWS

    +
    +public static final Jws2Client.Services ClustalWS
    +
    +
    +
    +
    +
    + +

    +TcoffeeWS

    +
    +public static final Jws2Client.Services TcoffeeWS
    +
    +
    +
    +
    +
    + +

    +ProbconsWS

    +
    +public static final Jws2Client.Services ProbconsWS
    +
    +
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +values

    +
    +public static Jws2Client.Services[] values()
    +
    +
    Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
    +for (Jws2Client.Services c : Jws2Client.Services.values())
+    System.out.println(c);
+
    +

    +

    + +
    Returns:
    an array containing the constants of this enum type, in +the order they are declared
    +
    +
    +
    + +

    +valueOf

    +
    +public static Jws2Client.Services valueOf(java.lang.String name)
    +
    +
    Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

    +

    +
    Parameters:
    name - the name of the enum constant to be returned. +
    Returns:
    the enum constant with the specified name +
    Throws: +
    java.lang.IllegalArgumentException - if this enum type has no constant +with the specified name +
    java.lang.NullPointerException - if the argument is null
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/Jws2Client.html b/website/full_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..97c55bf --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,375 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class Jws2Client

    +
    +java.lang.Object
+  extended by compbio.ws.client.Jws2Client
+
    +
    +
    +
    public class Jws2Client
    extends java.lang.Object
    + + +

    +A command line client for Jalview Web Services version 2 +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Nested Class Summary
    +static classJws2Client.Services + +
    +          List of web services currently supported by JWS2
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> MsaWS<T>
    +    		connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +static java.lang.StringgetHost(java.lang.String[] cmd) + +
    +          Extracts host name from the command line
    +static java.lang.StringgetServiceName(java.lang.String[] cmd) + +
    +          Extracts service name from the command line
    +static voidmain(java.lang.String[] args) + +
    +          Starts command line client, if no parameter are supported print help.
    +static booleanvalidURL(java.lang.String urlstr) + +
    +          Attempt to construct the URL object from the string
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Method Detail
    + +

    +validURL

    +
    +public static boolean validURL(java.lang.String urlstr)
    +
    +
    Attempt to construct the URL object from the string +

    +

    +
    Parameters:
    urlstr - +
    Returns:
    true if it succeed false otherwise
    +
    +
    +
    + +

    +getServiceName

    +
    +public static java.lang.String getServiceName(java.lang.String[] cmd)
    +
    +
    Extracts service name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    service name or null if it is not defined
    +
    +
    +
    + +

    +getHost

    +
    +public static java.lang.String getHost(java.lang.String[] cmd)
    +
    +
    Extracts host name from the command line +

    +

    +
    Parameters:
    cmd - command line options +
    Returns:
    host name or null if it is not defined
    +
    +
    +
    + +

    +connect

    +
    +public static <T> MsaWS<T> connect(java.lang.String host,
+                                   Jws2Client.Services service)
+                        throws javax.xml.ws.WebServiceException
    +
    +
    Connects to a web service by the host and the service name +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    host -
    service - +
    Returns:
    MsaWS +
    Throws: +
    javax.xml.ws.WebServiceException
    +
    +
    +
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    Starts command line client, if no parameter are supported print help. Two + parameters are required for successfull call the JWS2 host name and a + service name. +

    +

    +
    Parameters:
    args - Usage: -h=host_and_context + -s=serviceName ACTION [OPTIONS] + + -h= - a full URL to the JWS2 web server + including context path e.g. http://10.31.1.159:8080/ws + + -s= - one of [MafftWS, MuscleWS, ClustalWS, + TcoffeeWS, ProbconsWS] ACTIONS: + + -i= - full path to fasta formatted sequence file, + from which to align sequences + + -parameters - lists parameters supported by web service + + -presets - lists presets supported by web service + + -limits - lists web services limits Please note that if input + file is specified other actions are ignored + + OPTIONS: (only for use with -i action): + + -r= - name of the preset to use + + -o= - full path to the file where to write an + alignment -f= - the name of the file with + the list of parameters to use. Please note that -r and -f + options cannot be used together. Alignment is done with either + preset or a parameters from the file, but not both!
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/SimpleWSClient.html b/website/full_javadoc/compbio/ws/client/SimpleWSClient.html new file mode 100644 index 0000000..724fc81 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/SimpleWSClient.html @@ -0,0 +1,263 @@ + + + + + + +SimpleWSClient + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class SimpleWSClient

    +
    +java.lang.Object
+  extended by compbio.ws.client.SimpleWSClient
+
    +
    +
    +
    public class SimpleWSClient
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    SimpleWSClient() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SimpleWSClient

    +
    +public SimpleWSClient()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
+                 throws java.io.FileNotFoundException,
+                        java.io.IOException,
+                        JobSubmissionException,
+                        java.lang.InterruptedException,
+                        WrongParameterException
    +
    +
    + +
    Throws: +
    java.io.FileNotFoundException +
    java.io.IOException +
    JobSubmissionException +
    java.lang.InterruptedException +
    WrongParameterException
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/WSTester.html b/website/full_javadoc/compbio/ws/client/WSTester.html new file mode 100644 index 0000000..f138ed2 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/WSTester.html @@ -0,0 +1,275 @@ + + + + + + +WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.client +
    +Class WSTester

    +
    +java.lang.Object
+  extended by compbio.ws.client.WSTester
+
    +
    +
    +
    public class WSTester
    extends java.lang.Object
    + + +

    +Class for testing web services +

    + +

    +

    +
    Author:
    +
    pvtroshin + + Date February 2010
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSTester() + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> void
    +    		main(java.lang.String[] args) + +
    +          Test JWS2 web services
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WSTester

    +
    +public WSTester()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static <T> void main(java.lang.String[] args)
    +
    +
    Test JWS2 web services +

    +

    +
    Type Parameters:
    T - web service type
    Parameters:
    args - -h= + + -s= which is optional. If service name is not + provided then all known JWS2 web services are tested
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html new file mode 100644 index 0000000..7e5b0d6 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.Services.html @@ -0,0 +1,213 @@ + + + + + + +Uses of Class compbio.ws.client.Jws2Client.Services + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.Jws2Client.Services

    +
    + + + + + + + + + +
    +Packages that use Jws2Client.Services
    compbio.ws.client  
    +  +

    + + + + + +
    +Uses of Jws2Client.Services in compbio.ws.client
    +  +

    + + + + + + + + + + + + + +
    Methods in compbio.ws.client that return Jws2Client.Services
    +static Jws2Client.ServicesJws2Client.Services.valueOf(java.lang.String name) + +
    +          Returns the enum constant of this type with the specified name.
    +static Jws2Client.Services[]Jws2Client.Services.values() + +
    +          Returns an array containing the constants of this enum type, in +the order they are declared.
    +  +

    + + + + + + + + + +
    Methods in compbio.ws.client with parameters of type Jws2Client.Services
    +static + + + + +
    +<T> MsaWS<T>
    +    		Jws2Client.connect(java.lang.String host, + Jws2Client.Services service) + +
    +          Connects to a web service by the host and the service name
    +  +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html new file mode 100644 index 0000000..5b7e832 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/class-use/Jws2Client.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.Jws2Client + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.Jws2Client

    +
    +No usage of compbio.ws.client.Jws2Client +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html b/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html new file mode 100644 index 0000000..21628f6 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/class-use/SimpleWSClient.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.SimpleWSClient + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.SimpleWSClient

    +
    +No usage of compbio.ws.client.SimpleWSClient +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/class-use/WSTester.html b/website/full_javadoc/compbio/ws/client/class-use/WSTester.html new file mode 100644 index 0000000..3c10d3a --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/class-use/WSTester.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.client.WSTester + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + +
    +
    +

    +Uses of Class
    compbio.ws.client.WSTester

    +
    +No usage of compbio.ws.client.WSTester +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/client/package-frame.html b/website/full_javadoc/compbio/ws/client/package-frame.html new file mode 100644 index 0000000..3b26d63 --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/package-frame.html @@ -0,0 +1,45 @@ + + + + + + +compbio.ws.client + + + + + + + + + + + +compbio.ws.client + + + + +
    +Classes  + +
    +Jws2Client +
    +WSTester
    + + + + + + +
    +Enums  + +
    +Jws2Client.Services
    + + + + diff --git a/website/full_javadoc/compbio/ws/client/package-summary.html b/website/full_javadoc/compbio/ws/client/package-summary.html new file mode 100644 index 0000000..bd6a63a --- /dev/null +++ b/website/full_javadoc/compbio/ws/client/package-summary.html @@ -0,0 +1,175 @@ + + + + + + +compbio.ws.client + + + + + + + + + + + + +
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    +Package compbio.ws.client +

    + + + + + + + + + + + + + +
    +Class Summary
    Jws2ClientA command line client for Jalview Web Services version 2
    WSTesterClass for testing web services
    +  + +

    + + + + + + + + + +
    +Enum Summary
    Jws2Client.ServicesList of web services currently supported by JWS2
    +  + +

    +

    +
    +
    + + + + + + + + + + + + + + + +
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    +Hierarchy For Package compbio.ws.client +

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    Package Hierarchies:
    All Packages
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      +
    • java.lang.Object
        +
      • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable) + +
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    +Uses of Package
    compbio.ws.client

    +
    + + + + + + + + + +
    +Packages that use compbio.ws.client
    compbio.ws.client  
    +  +

    + + + + + + + + +
    +Classes in compbio.ws.client used by compbio.ws.client
    Jws2Client.Services + +
    +          List of web services currently supported by JWS2
    +  +

    +

    + + + + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/ClustalWS.html b/website/full_javadoc/compbio/ws/server/ClustalWS.html new file mode 100644 index 0000000..09d7072 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/ClustalWS.html @@ -0,0 +1,599 @@ + + + + + + +ClustalWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class ClustalWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.ClustalWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<ClustalW>
    +
    +
    +
    +
    public class ClustalWS
    extends java.lang.Object
    implements MsaWS<ClustalW>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ClustalWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<ClustalW>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<ClustalW>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<ClustalW>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<ClustalW>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<ClustalW>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<ClustalW> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ClustalWS

    +
    +public ClustalWS()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Specified by:
    align in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<ClustalW> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Specified by:
    presetAlign in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<ClustalW>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with options. +

    +

    +
    Specified by:
    customAlign in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<ClustalW> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    Specified by:
    getResult in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<ClustalW> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<ClustalW> getLimits()
    +
    +
    Description copied from interface: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<ClustalW> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<ClustalW>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Specified by:
    pullExecStatistics in interface MsaWS<ClustalW>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/MafftWS.html b/website/full_javadoc/compbio/ws/server/MafftWS.html new file mode 100644 index 0000000..d419846 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/MafftWS.html @@ -0,0 +1,599 @@ + + + + + + +MafftWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class MafftWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.MafftWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Mafft>
    +
    +
    +
    +
    public class MafftWS
    extends java.lang.Object
    implements MsaWS<Mafft>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    MafftWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Mafft>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Mafft>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<Mafft>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<Mafft>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Mafft>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Mafft> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +MafftWS

    +
    +public MafftWS()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Specified by:
    align in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Mafft>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with options. +

    +

    +
    Specified by:
    customAlign in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Mafft> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Specified by:
    presetAlign in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    Specified by:
    getResult in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Mafft> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Mafft> getLimits()
    +
    +
    Description copied from interface: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Specified by:
    pullExecStatistics in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Mafft>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Mafft> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Mafft> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<Mafft>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/MuscleWS.html b/website/full_javadoc/compbio/ws/server/MuscleWS.html new file mode 100644 index 0000000..0d9ec95 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/MuscleWS.html @@ -0,0 +1,599 @@ + + + + + + +MuscleWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class MuscleWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.MuscleWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Muscle>
    +
    +
    +
    +
    public class MuscleWS
    extends java.lang.Object
    implements MsaWS<Muscle>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    MuscleWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Muscle>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Muscle>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<Muscle>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<Muscle>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Muscle>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Muscle> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +MuscleWS

    +
    +public MuscleWS()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Specified by:
    align in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Muscle>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with options. +

    +

    +
    Specified by:
    customAlign in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Muscle> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Specified by:
    presetAlign in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    Specified by:
    getResult in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Muscle> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Muscle> getLimits()
    +
    +
    Description copied from interface: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Specified by:
    pullExecStatistics in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Muscle>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Muscle> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Muscle> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<Muscle>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/ProbconsWS.html b/website/full_javadoc/compbio/ws/server/ProbconsWS.html new file mode 100644 index 0000000..a97b8eb --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/ProbconsWS.html @@ -0,0 +1,599 @@ + + + + + + +ProbconsWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class ProbconsWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.ProbconsWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Probcons>
    +
    +
    +
    +
    public class ProbconsWS
    extends java.lang.Object
    implements MsaWS<Probcons>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    ProbconsWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Probcons>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Probcons>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<Probcons>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<Probcons>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Probcons>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Probcons> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +ProbconsWS

    +
    +public ProbconsWS()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Specified by:
    align in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Probcons>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with options. +

    +

    +
    Specified by:
    customAlign in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Probcons> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Specified by:
    presetAlign in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    Specified by:
    getResult in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Probcons> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Probcons> getLimits()
    +
    +
    Description copied from interface: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Specified by:
    pullExecStatistics in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Probcons>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Probcons> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Probcons> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<Probcons>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html new file mode 100644 index 0000000..e4fd0ac --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/SimpleWSPublisher.html @@ -0,0 +1,263 @@ + + + + + + +SimpleWSPublisher + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class SimpleWSPublisher

    +
    +java.lang.Object
+  extended by compbio.ws.server.SimpleWSPublisher
+
    +
    +
    +
    public class SimpleWSPublisher
    extends java.lang.Object
    + + +

    +This class publish a web service. This is not a production implementation. + Should be used only for during development and testing +

    + +

    +

    +
    Author:
    +
    pvtroshin
    +
    +
    + +

    + + + + + + + + + + + +
    +Constructor Summary
    SimpleWSPublisher(java.lang.Object exec, + java.lang.String context) + +
    +           
    +  + + + + + + + + + + + +
    +Method Summary
    +static voidmain(java.lang.String[] args) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +SimpleWSPublisher

    +
    +public SimpleWSPublisher(java.lang.Object exec,
+                         java.lang.String context)
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +main

    +
    +public static void main(java.lang.String[] args)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/TcoffeeWS.html b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html new file mode 100644 index 0000000..bc9ed89 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/TcoffeeWS.html @@ -0,0 +1,599 @@ + + + + + + +TcoffeeWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class TcoffeeWS

    +
    +java.lang.Object
+  extended by compbio.ws.server.TcoffeeWS
+
    +
    +
    All Implemented Interfaces:
    MsaWS<Tcoffee>
    +
    +
    +
    +
    public class TcoffeeWS
    extends java.lang.Object
    implements MsaWS<Tcoffee>
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    TcoffeeWS() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    + java.lang.Stringalign(java.util.List<FastaSequence> sequences) + +
    +          Align a list of sequences with default settings.
    + booleancancelJob(java.lang.String jobId) + +
    +          Stop running job but leave its output untouched
    + java.lang.StringcustomAlign(java.util.List<FastaSequence> sequences, + java.util.List<Option<Tcoffee>> options) + +
    +          Align a list of sequences with options.
    + JobStatusgetJobStatus(java.lang.String jobId) + +
    +          Return the status of the job.
    + Limit<Tcoffee>getLimit(java.lang.String presetName) + +
    +          Get a Limit for a preset.
    + LimitsManager<Tcoffee>getLimits() + +
    +          List Limits supported by a web service.
    + PresetManager<Tcoffee>getPresets() + +
    +          Get presets supported by a web service
    + AlignmentgetResult(java.lang.String jobId) + +
    +          Return the result of the job.
    + RunnerConfig<Tcoffee>getRunnerOptions() + +
    +          Get options supported by a web service
    + java.lang.StringpresetAlign(java.util.List<FastaSequence> sequences, + Preset<Tcoffee> preset) + +
    +          Align a list of sequences with preset.
    + ChunkHolderpullExecStatistics(java.lang.String jobId, + long position) + +
    +          Reads 1kb chunk from the statistics file which is specific to a given web + service from the position.
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +TcoffeeWS

    +
    +public TcoffeeWS()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +align

    +
    +public java.lang.String align(java.util.List<FastaSequence> sequences)
+                       throws JobSubmissionException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with default settings. + + Any dataset containing a greater number of sequences or the average + length of the sequences are greater then defined in the default Limit + will not be accepted for an alignment operation and + JobSubmissionException will be thrown. +

    +

    +
    Specified by:
    align in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    JobSubmissionException
    +
    +
    +
    + +

    +customAlign

    +
    +public java.lang.String customAlign(java.util.List<FastaSequence> sequences,
+                                    java.util.List<Option<Tcoffee>> options)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with options. +

    +

    +
    Specified by:
    customAlign in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    options - A list of Options +
    Returns:
    jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    See Also:
    Default Limit is used to decide whether the calculation will be + permitted or denied
    +
    +
    +
    + +

    +presetAlign

    +
    +public java.lang.String presetAlign(java.util.List<FastaSequence> sequences,
+                                    Preset<Tcoffee> preset)
+                             throws JobSubmissionException,
+                                    WrongParameterException
    +
    +
    Description copied from interface: MsaWS
    +
    Align a list of sequences with preset. @see Preset + + Limit for a presetName is used whether the calculation will be permitted + or denied. If no Limit was defined for a presetName, than default limit + is used. +

    +

    +
    Specified by:
    presetAlign in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    sequences - List of FastaSequence objects. The programme does not perform + any sequence validity checks. Nor does it checks whether the + sequences names are unique. It is responsibility of the caller + to validate this information
    preset - A list of Options +
    Returns:
    String - jobId - unique identifier for the job +
    Throws: +
    UnsupportedRuntimeException - thrown if server OS does not support native executables for a + given web service, e.g. JWS2 is deployed on Windows and Mafft + service is called +
    LimitExceededException - is throw if the input sequences number or average length + exceeds what is defined by the limit +
    WrongParameterException - is throws when 1) One of the Options provided is not + supported, 2) The value of the option is defined outside the + boundaries. In both cases exception object contain the + information on the violating Option. +
    JobSubmissionException
    +
    +
    +
    + +

    +getResult

    +
    +public Alignment getResult(java.lang.String jobId)
+                    throws ResultNotAvailableException
    +
    +
    Description copied from interface: MsaWS
    +
    Return the result of the job. +

    +

    +
    Specified by:
    getResult in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    jobId - a unique job identifier +
    Returns:
    Alignment +
    Throws: +
    ResultNotAvailableException - this exception is throw if the job execution was not + successful or the result of the execution could not be found. + (e.g. removed). Exception could also be thrown is dues to the + lower level problems on the server i.e. IOException, + FileNotFoundException problems as well as + UnknownFileFormatException.
    +
    +
    +
    + +

    +getLimit

    +
    +public Limit<Tcoffee> getLimit(java.lang.String presetName)
    +
    +
    Description copied from interface: MsaWS
    +
    Get a Limit for a preset. +

    +

    +
    Specified by:
    getLimit in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    presetName - the name of the preset. if no name is provided, then the + default preset is returned. If no limit for a particular + preset is defined then the default preset is returned +
    Returns:
    Limit
    +
    +
    +
    + +

    +getLimits

    +
    +public LimitsManager<Tcoffee> getLimits()
    +
    +
    Description copied from interface: MsaWS
    +
    List Limits supported by a web service. +

    +

    +
    Specified by:
    getLimits in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    LimitManager
    +
    +
    +
    + +

    +pullExecStatistics

    +
    +public ChunkHolder pullExecStatistics(java.lang.String jobId,
+                                      long position)
    +
    +
    Description copied from interface: MsaWS
    +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. If in time of a request less then 1kb data is + available from the position to the end of the file, then it returns all + the data available from the position to the end of the file. +

    +

    +
    Specified by:
    pullExecStatistics in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier
    position - - next position within the file to read +
    Returns:
    ChunkHolder - @see ChunkHolder which contains a chuink of data + and a next position within the file from which no data has been + read
    +
    +
    +
    + +

    +cancelJob

    +
    +public boolean cancelJob(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Stop running job but leave its output untouched +

    +

    +
    Specified by:
    cancelJob in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    true if job was cancelled successfully, false otherwise
    +
    +
    +
    + +

    +getJobStatus

    +
    +public JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    Description copied from interface: MsaWS
    +
    Return the status of the job. @see JobStatus +

    +

    +
    Specified by:
    getJobStatus in interface MsaWS<Tcoffee>
    +
    +
    +
    Parameters:
    jobId - - unique job identifier +
    Returns:
    JobStatus - status of the job
    +
    +
    +
    + +

    +getPresets

    +
    +public PresetManager<Tcoffee> getPresets()
    +
    +
    Description copied from interface: MsaWS
    +
    Get presets supported by a web service +

    +

    +
    Specified by:
    getPresets in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    PresetManager the object contains information about presets + supported by a web service
    +
    +
    +
    + +

    +getRunnerOptions

    +
    +public RunnerConfig<Tcoffee> getRunnerOptions()
    +
    +
    Description copied from interface: MsaWS
    +
    Get options supported by a web service +

    +

    +
    Specified by:
    getRunnerOptions in interface MsaWS<Tcoffee>
    +
    +
    + +
    Returns:
    RunnerConfig the list of options and parameters supported by a + web service.
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/WSUtil.html b/website/full_javadoc/compbio/ws/server/WSUtil.html new file mode 100644 index 0000000..cb07ea7 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/WSUtil.html @@ -0,0 +1,510 @@ + + + + + + +WSUtil + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
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    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + +

    + +compbio.ws.server +
    +Class WSUtil

    +
    +java.lang.Object
+  extended by compbio.ws.server.WSUtil
+
    +
    +
    +
    public final class WSUtil
    extends java.lang.Object
    + + +

    +

    + +

    + + + + + + + + + + + +
    +Constructor Summary
    WSUtil() + +
    +           
    +  + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +Method Summary
    +static + + + + +
    +<T> java.lang.String
    +    		align(java.util.List<FastaSequence> sequences, + ConfiguredExecutable<T> confExec, + org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String callingMethod, + Limit<T> limit) + +
    +           
    +static booleancancelJob(java.lang.String jobId) + +
    +           
    +static + + + + +
    +<T> java.util.List<java.lang.String>
    +    		getCommands(java.util.List<Option<T>> options, + java.lang.String keyValueSeparator) + +
    +           
    +static AsyncExecutorgetEngine(ConfiguredExecutable<?> confClustal) + +
    +           
    +static JobStatusgetJobStatus(java.lang.String jobId) + +
    +           
    +static bytegetProgress(java.lang.String jobId) + +
    +           
    +static java.lang.StringgetRemoteAddress(javax.xml.ws.WebServiceContext wsContext) + +
    +           
    +static voidlog(org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String activity) + +
    +           
    +static voidlog(org.apache.log4j.Logger statLog, + javax.xml.ws.WebServiceContext wsContext, + java.lang.String jobId, + java.lang.String activity) + +
    +           
    +static ChunkHolderpullFile(java.lang.String jobId, + long position) + +
    +           
    +static voidvalidateFastaInput(java.util.List<FastaSequence> sequences) + +
    +           
    +static voidvalidateJobId(java.lang.String jobId) + +
    +           
    +  + + + + + + + +
    Methods inherited from class java.lang.Object
    equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    +  +

    + + + + + + + + +
    +Constructor Detail
    + +

    +WSUtil

    +
    +public WSUtil()
    +
    +
    + + + + + + + + +
    +Method Detail
    + +

    +log

    +
    +public static void log(org.apache.log4j.Logger statLog,
+                       javax.xml.ws.WebServiceContext wsContext,
+                       java.lang.String activity)
    +
    +
    +
    +
    +
    +
    + +

    +validateJobId

    +
    +public static final void validateJobId(java.lang.String jobId)
+                                throws java.security.InvalidParameterException
    +
    +
    + +
    Throws: +
    java.security.InvalidParameterException
    +
    +
    +
    + +

    +validateFastaInput

    +
    +public static final void validateFastaInput(java.util.List<FastaSequence> sequences)
+                                     throws java.security.InvalidParameterException
    +
    +
    + +
    Throws: +
    java.security.InvalidParameterException
    +
    +
    +
    + +

    +log

    +
    +public static void log(org.apache.log4j.Logger statLog,
+                       javax.xml.ws.WebServiceContext wsContext,
+                       java.lang.String jobId,
+                       java.lang.String activity)
    +
    +
    +
    +
    +
    +
    + +

    +getJobStatus

    +
    +public static JobStatus getJobStatus(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +pullFile

    +
    +public static ChunkHolder pullFile(java.lang.String jobId,
+                                   long position)
    +
    +
    +
    +
    +
    +
    + +

    +getProgress

    +
    +public static byte getProgress(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +getEngine

    +
    +public static AsyncExecutor getEngine(ConfiguredExecutable<?> confClustal)
    +
    +
    +
    +
    +
    +
    + +

    +cancelJob

    +
    +public static boolean cancelJob(java.lang.String jobId)
    +
    +
    +
    +
    +
    +
    + +

    +getRemoteAddress

    +
    +public static java.lang.String getRemoteAddress(javax.xml.ws.WebServiceContext wsContext)
    +
    +
    +
    +
    +
    +
    + +

    +align

    +
    +public static <T> java.lang.String align(java.util.List<FastaSequence> sequences,
+                                         ConfiguredExecutable<T> confExec,
+                                         org.apache.log4j.Logger statLog,
+                                         javax.xml.ws.WebServiceContext wsContext,
+                                         java.lang.String callingMethod,
+                                         Limit<T> limit)
+                              throws LimitExceededException,
+                                     JobSubmissionException
    +
    +
    + +
    Throws: +
    LimitExceededException +
    JobSubmissionException
    +
    +
    +
    + +

    +getCommands

    +
    +public static final <T> java.util.List<java.lang.String> getCommands(java.util.List<Option<T>> options,
+                                                                     java.lang.String keyValueSeparator)
    +
    +
    +
    +
    +
    + +
    + + + + + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
    + SUMMARY: NESTED | FIELD | CONSTR | METHOD +DETAIL: FIELD | CONSTR | METHOD
    + + + +
    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html b/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html new file mode 100644 index 0000000..b33dc12 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/ClustalWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.ClustalWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class   Use  Tree  Deprecated  Index  Help 
    +    		 + +
    + PREV  + NEXT + FRAMES   + NO FRAMES   +  + + + +
    + + + +
    +
    +

    +Uses of Class
    compbio.ws.server.ClustalWS

    +
    +No usage of compbio.ws.server.ClustalWS +

    +

    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    + + + diff --git a/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html b/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html new file mode 100644 index 0000000..5b7bfba --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/class-use/MafftWS.html @@ -0,0 +1,144 @@ + + + + + + +Uses of Class compbio.ws.server.MafftWS + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +Classes  + +
    +ClustalWS +
    +MafftWS +
    +MuscleWS +
    +ProbconsWS +
    +SimpleWSPublisher +
    +TcoffeeWS +
    +WSUtil
    + + + + diff --git a/website/full_javadoc/compbio/ws/server/package-summary.html b/website/full_javadoc/compbio/ws/server/package-summary.html new file mode 100644 index 0000000..4937713 --- /dev/null +++ b/website/full_javadoc/compbio/ws/server/package-summary.html @@ -0,0 +1,181 @@ + + + + + + +compbio.ws.server + + + + + + + + + + + + +
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    +Package compbio.ws.server +

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    +Class Summary
    ClustalWS 
    MafftWS 
    MuscleWS 
    ProbconsWS 
    SimpleWSPublisherThis class publish a web service.
    TcoffeeWS 
    WSUtil 
    +  + +

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    +compbio.data.*
    + +

    + + + + + + + + + + + + +
    compbio.data.sequence.ClustalAlignmentUtil
    +public static final chargapchar45
    + +

    + +

    + + + + + +
    +compbio.engine.*
    + +

    + + + + + + + + + + + + +
    compbio.engine.client.ConfExecutable<T>
    +public static final java.lang.StringCLUSTER_TASK_ID_PREFIX"@"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.client.EnvVariableProcessor
    +public static final java.lang.StringPATH"PATH"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.client.RunConfiguration
    +public static final java.lang.StringrconfigFile"RunnerConfig.xml"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.cluster.drmaa.ClusterSession
    +public static final java.lang.StringJOBID"JOBID"
    + +

    + +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    compbio.engine.cluster.dundee._QueueConstraints
    +public static final intFIRST_MEMORY_LIMIT14000
    +public static final intLONG_TIME_LIMIT24
    +public static final intMAX_MEMORY_LIMIT30000
    +public static final intSHORT_TIME_LIMIT8
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.conf._Key
    +public static final java.lang.StringDELIM"#"
    + +

    + +

    + + + + + + + + + + + + +
    compbio.engine.conf.DirectoryManager
    +public static final java.lang.StringDELIM"#"
    + +

    + +

    + + + + + + + + + + + + + + + + + +
    compbio.engine.local.ExecutableWrapper
    +public static final java.lang.StringPROC_ERR_FILE"procError.txt"
    +public static final java.lang.StringPROC_OUT_FILE"procOutput.txt"
    + +

    + +

    + + + + + +
    +compbio.metadata.*
    + +

    + + + + + + + + + + + + +
    compbio.metadata.PresetManager<T>
    +public static final java.lang.StringLOCAL_ENGINE_LIMIT_PRESET"# LocalEngineExecutionLimit #"
    + +

    + +

    + + + + + +
    +compbio.runner.*
    + +

    + + + + + + + + + + + + +
    compbio.runner.Util
    +public static final java.lang.StringSPACE" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.ClustalW
    +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Mafft
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Muscle
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Probcons
    +public static final java.lang.StringKEY_VALUE_SEPARATOR" "
    + +

    + +

    + + + + + + + + + + + + +
    compbio.runner.msa.Tcoffee
    +public static final java.lang.StringKEY_VALUE_SEPARATOR"="
    + +

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    +Deprecated Methods
    compbio.engine.cluster.drmaa.ClusterSession.getJobStatus(int) +
    +           
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    + + + +A B C D E F G H I J K L M N O P R S T U V W _
    +

    +A

    +
    +
    AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Valid Amino acids +
    addOption(Option<T>) - +Method in class compbio.metadata.RunnerConfig +
      +
    addOptionNames(String...) - +Method in class compbio.metadata.Option +
    Adds an option to the optionName list +
    addOptionNames(String...) - +Method in class compbio.metadata.Parameter +
      +
    addParameter(Parameter<T>) - +Method in class compbio.metadata.RunnerConfig +
      +
    addParameter(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    addParameters(List<String>) - +Method in class compbio.engine.client.ConfExecutable +
      +
    addParameters(List<String>) - +Method in interface compbio.engine.client.Executable +
    Adds parameter to the list of parameters for a native executable +
    addParameters(List<String>) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    addParameters(List<String>) - +Method in class compbio.runner._impl.NetNglyc +
      +
    addParameters(String[]) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    addParameters(List<String>) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    addParameters(List<String>) - +Method in class compbio.runner.msa.Mafft +
    Mafft input must always be the last parameter! +
    addParams(List<String>) - +Method in class compbio.engine.client.CommandBuilder +
      +
    addPossibleValues(String...) - +Method in class compbio.metadata.Parameter +
      +
    addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - +Static method in class compbio.engine.SubmissionManager +
      +
    Align - Class in compbio.data.msa.jaxws
     
    Align() - +Constructor for class compbio.data.msa.jaxws.Align +
      +
    align(List<FastaSequence>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with default settings. +
    align(List<FastaSequence>) - +Method in class compbio.ws.server.ClustalWS +
      +
    align(List<FastaSequence>) - +Method in class compbio.ws.server.MafftWS +
      +
    align(List<FastaSequence>) - +Method in class compbio.ws.server.MuscleWS +
      +
    align(List<FastaSequence>) - +Method in class compbio.ws.server.ProbconsWS +
      +
    align(List<FastaSequence>) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, WebServiceContext, String, Limit<T>) - +Static method in class compbio.ws.server.WSUtil +
      +
    Alignment - Class in compbio.data.sequence
    Multiple sequence alignment.
    Alignment(List<FastaSequence>, Program, char) - +Constructor for class compbio.data.sequence.Alignment +
      +
    Alignment(List<FastaSequence>, AlignmentMetadata) - +Constructor for class compbio.data.sequence.Alignment +
      +
    AlignmentMetadata - Class in compbio.data.sequence
    Alignment metadata e.g.
    AlignmentMetadata(Program, char) - +Constructor for class compbio.data.sequence.AlignmentMetadata +
      +
    AlignResponse - Class in compbio.data.msa.jaxws
     
    AlignResponse() - +Constructor for class compbio.data.msa.jaxws.AlignResponse +
      +
    AMBIGUOUS_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    Same as AA pattern but with two additional letters - XU +
    AMBIGUOUS_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Ambiguous nucleotide +
    Argument<T> - Interface in compbio.metadata
    An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
    argumentsToCommandString(List<? extends Option<?>>) - +Method in class compbio.runner.OptionCombinator +
      +
    argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - +Static method in class compbio.runner.OptionCombinator +
      +
    AsyncExecutor - Interface in compbio.engine
    An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
    AsyncJobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    AsyncJobRunner() - +Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    AsyncLocalRunner - Class in compbio.engine.local
     
    AsyncLocalRunner() - +Constructor for class compbio.engine.local.AsyncLocalRunner +
      +
    awaitTermination(long, TimeUnit) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    +
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    +
    JnetAnnotation - Enum in compbio.data._structure
     
    Job - Class in compbio.engine
     
    Job(String, String, ConfiguredExecutable<?>) - +Constructor for class compbio.engine.Job +
      +
    JobExecutionException - Exception in compbio.metadata
    JobExecutionException is thrown wherever the results of the calculation + cannot be obtained.
    JobExecutionException(String) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionException(String, Throwable) - +Constructor for exception compbio.metadata.JobExecutionException +
      +
    JobExecutionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobExecutionExceptionBean() - +Constructor for class compbio.data.msa.jaxws.JobExecutionExceptionBean +
      +
    JOBID - +Static variable in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    JobRunner - Class in compbio.engine.cluster.drmaa
    Single cluster job runner class
    JobRunner(ConfiguredExecutable<?>) - +Constructor for class compbio.engine.cluster.drmaa.JobRunner +
      +
    JobStatus - Enum in compbio.metadata
    The status of the job.
    JobSubmissionException - Exception in compbio.metadata
    Exception for generic problems with JobSubmission it is often thrown as a + wrapper for the lower level exceptions like IOException or DrmaaException.
    JobSubmissionException(String) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionException(String, Throwable) - +Constructor for exception compbio.metadata.JobSubmissionException +
      +
    JobSubmissionExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    JobSubmissionExceptionBean() - +Constructor for class compbio.data.msa.jaxws.JobSubmissionExceptionBean +
      +
    Jpred4 - Class in compbio.pipeline._jpred
    jpred --sequence OR --alignment [--db + ] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help] + + jpred4 --sequence The path to the sequence (in FASTA format) you + want to predict OR + + [--alignment ] The alignment which to use for prediction + + [--profile=] + + [--db ] Database to use for PSI-BLAST querying.
    Jpred4() - +Constructor for class compbio.pipeline._jpred.Jpred4 +
      +
    JpredAnnotation - Enum in compbio.data._structure
     
    JpredResult - Class in compbio.data._structure
    Jnet result + + jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H + ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H, + -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,- + , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7, + 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9 + 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7 + , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,- + , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,- + ,B, + JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,- + ,-,- + JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-, + -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-, + JNETHMM:-,H,H,H,H,H,H,H,H,H,H, + H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-, + -,-,-,-,-,-,-,-,-,-,-,-,-,-,- + ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H, + JNETPROPH:0.0110,0.1125,0.8552,0.0107 + ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120 + ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244 + ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017, + JNETPROPE:0.0107,0.6245,0.3614,0.0120 + ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102 + ,0.9586,0.0465,0.0094,0.9662,0.0433, + ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,
    JpredResult() - +Constructor for class compbio.data._structure.JpredResult +
      +
    Jws2Client - Class in compbio.ws.client
    A command line client for Jalview Web Services version 2
    Jws2Client.Services - Enum in compbio.ws.client
    List of web services currently supported by JWS2
    +
    + + + + + + + + + + + + + + + +
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    +
    +
    KEY_VALUE_SEPARATOR - +Static variable in class compbio.runner.msa.ClustalW +
      +
    KEY_VALUE_SEPARATOR - +Static variable in class compbio.runner.msa.Mafft +
      +
    KEY_VALUE_SEPARATOR - +Static variable in class compbio.runner.msa.Muscle +
      +
    KEY_VALUE_SEPARATOR - +Static variable in class compbio.runner.msa.Probcons +
      +
    KEY_VALUE_SEPARATOR - +Static variable in class compbio.runner.msa.Tcoffee +
      +
    +
    + + + + + + + + + + + + + + + +
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    +
    Limit<T> - Class in compbio.metadata
    A value object containing a maximum number of sequences and a maximum average + sequence length for a preset.
    Limit(int, int, String) - +Constructor for class compbio.metadata.Limit +
      +
    Limit(int, int, String, boolean) - +Constructor for class compbio.metadata.Limit +
      +
    LimitExceededException - Exception in compbio.metadata
    Thrown if the task larger in size that the limit that applies to the + calculation.
    LimitExceededException(String) - +Constructor for exception compbio.metadata.LimitExceededException +
      +
    LimitExceededExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    LimitExceededExceptionBean() - +Constructor for class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    LimitsManager<T> - Class in compbio.metadata
    A collection of Limits
    LimitsManager() - +Constructor for class compbio.metadata.LimitsManager +
      +
    load(InputStream) - +Static method in class compbio.engine.client.RunConfiguration +
      +
    LoadBalancer - Class in compbio.engine
     
    loadExecutable(String) - +Static method in class compbio.engine.client.Util +
      +
    loadRunConfiguration(RunConfiguration) - +Method in class compbio.engine.client.ConfExecutable +
      +
    loadRunConfiguration(InputStream) - +Method in class compbio.engine.client.ConfExecutable +
      +
    loadRunConfiguration(InputStream) - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    loadRunConfiguration(RunConfiguration) - +Method in interface compbio.engine.client.Executable +
      +
    loadRunConfiguration(RunConfiguration) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    loadRunConfiguration(RunConfiguration) - +Method in class compbio.runner._impl.NetNglyc +
      +
    loadRunConfiguration(RunConfiguration) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    LOCAL_ENGINE_LIMIT_PRESET - +Static variable in class compbio.metadata.PresetManager +
      +
    LOCAL_WORK_DIRECTORY - +Static variable in class compbio.engine.Configurator +
      +
    LocalEngineUtil - Class in compbio.engine.local
     
    LocalEngineUtil() - +Constructor for class compbio.engine.local.LocalEngineUtil +
      +
    LocalExecutorService - Class in compbio.engine.local
     
    LocalRunner - Class in compbio.engine.local
     
    LocalRunner(ConfiguredExecutable<?>) - +Constructor for class compbio.engine.local.LocalRunner +
      +
    log(Logger, WebServiceContext, String) - +Static method in class compbio.ws.server.WSUtil +
      +
    log(Logger, WebServiceContext, String, String) - +Static method in class compbio.ws.server.WSUtil +
      +
    LONG_TIME_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    Mafft - Class in compbio.runner.msa
     
    Mafft() - +Constructor for class compbio.runner.msa.Mafft +
      +
    MafftWS - Class in compbio.ws.server
     
    MafftWS() - +Constructor for class compbio.ws.server.MafftWS +
      +
    main(String[]) - +Static method in class compbio.engine.cluster.drmaa._DrmaaExample +
      +
    main(String[]) - +Static method in class compbio.engine.cluster.drmaa._JobStatus +
      +
    main(String[]) - +Static method in class compbio.pipeline._jpred.BlastParser +
    args[0] is assumed to be the name of a Blast output file +
    main(String[]) - +Static method in class compbio.pipeline._jpred.Pairwise +
      +
    main(String[]) - +Static method in class compbio.runner._impl.OB +
      +
    main(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Starts command line client, if no parameter are supported print help. +
    main(String[]) - +Static method in class compbio.ws.client.WSTester +
    Test JWS2 web services +
    main(String[]) - +Static method in class compbio.ws.server.SimpleWSPublisher +
      +
    MAX_MEMORY_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    Mcl - Class in compbio.runner._impl
     
    Mcl(String) - +Constructor for class compbio.runner._impl.Mcl +
      +
    mergeEnvVariables(Map<String, String>, Map<String, String>) - +Static method in class compbio.engine.client.Util +
      +
    MsaWS<T> - Interface in compbio.data.msa
    Multiple Sequence Alignment (MSA) Web Services Interface
    Muscle - Class in compbio.runner.msa
     
    Muscle() - +Constructor for class compbio.runner.msa.Muscle +
    Default options are + + -clwstrict - write output in clustal format +
    MuscleWS - Class in compbio.ws.server
     
    MuscleWS() - +Constructor for class compbio.ws.server.MuscleWS +
      +
    +
    + + + + + + + + + + + + + + + +
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    +
    NetNglyc - Class in compbio.runner._impl
     
    NetNglyc() - +Constructor for class compbio.runner._impl.NetNglyc +
      +
    newCommandBuilder(List<? extends Option<T>>, String) - +Static method in class compbio.engine.client.CommandBuilder +
    This produces the same result as getCommands method. +
    newConfExecutable(RunConfiguration) - +Static method in class compbio.engine.client.ConfExecutable +
      +
    newFilePuller(String, int) - +Static method in class compbio.engine.FilePuller +
      +
    newLimitExceeded(Limit<?>, List<FastaSequence>) - +Static method in exception compbio.metadata.LimitExceededException +
      +
    newProgressPuller(String) - +Static method in class compbio.engine.FilePuller +
    Progress Puller is designed to read 3 characters from the beginning of + the file, nothing more. +
    NON_AA - +Static variable in class compbio.data.sequence.SequenceUtil +
    inversion of AA pattern +
    NON_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non nucleotide +
    NONWORD - +Static variable in class compbio.data.sequence.SequenceUtil +
    Non word +
    NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +
    Nucleotides a, t, g, c, u +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +O

    +
    +
    OB - Class in compbio.runner._impl
    TODO this needs fixing! Executable does not work
    OB() - +Constructor for class compbio.runner._impl.OB +
      +
    OB(String) - +Constructor for class compbio.runner._impl.OB +
      +
    Option<T> - Class in compbio.metadata
    Command line option/flag or multiple exclusive options with no value.
    Option(String, String) - +Constructor for class compbio.metadata.Option +
      +
    OptionCombinator - Class in compbio.runner
    This class solve the following problems.
    OptionCombinator(RunnerConfig<? extends Executable<?>>) - +Constructor for class compbio.runner.OptionCombinator +
      +
    optionsToCommandString(List<Option<?>>) - +Method in class compbio.runner.OptionCombinator +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    Pairwise - Class in compbio.pipeline._jpred
     
    Pairwise(List<FastaSequence>) - +Constructor for class compbio.pipeline._jpred.Pairwise +
      +
    Parameter<T> - Class in compbio.metadata
    A single value containing option supported by the web service e.g.
    Parameter(String, String) - +Constructor for class compbio.metadata.Parameter +
      +
    parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - +Method in class compbio.runner.OptionCombinator +
      +
    parse(String) - +Static method in class compbio.engine.conf._Key +
      +
    PATH - +Static variable in class compbio.engine.client.EnvVariableProcessor +
    Special variable keys Absolute path(s) will be merged with the content of + the system PATH variable +
    PathValidator - Class in compbio.engine.client
     
    PathValidator() - +Constructor for class compbio.engine.client.PathValidator +
      +
    PipedExecutable<T> - Interface in compbio.engine.client
    This is a marker interface to indicate that the output of the process must be + captured.
    Preset<T> - Class in compbio.metadata
    Collection of Options and Parameters with their values
    Preset() - +Constructor for class compbio.metadata.Preset +
      +
    PresetAlign - Class in compbio.data.msa.jaxws
     
    PresetAlign() - +Constructor for class compbio.data.msa.jaxws.PresetAlign +
      +
    presetAlign(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with preset. +
    presetAlign(List<FastaSequence>, Preset<ClustalW>) - +Method in class compbio.ws.server.ClustalWS +
      +
    presetAlign(List<FastaSequence>, Preset<Mafft>) - +Method in class compbio.ws.server.MafftWS +
      +
    presetAlign(List<FastaSequence>, Preset<Muscle>) - +Method in class compbio.ws.server.MuscleWS +
      +
    presetAlign(List<FastaSequence>, Preset<Probcons>) - +Method in class compbio.ws.server.ProbconsWS +
      +
    presetAlign(List<FastaSequence>, Preset<Tcoffee>) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    PresetAlignResponse - Class in compbio.data.msa.jaxws
     
    PresetAlignResponse() - +Constructor for class compbio.data.msa.jaxws.PresetAlignResponse +
      +
    PresetManager<T> - Class in compbio.metadata
    Collection of presets and methods to manipulate them @see Preset
    PresetManager() - +Constructor for class compbio.metadata.PresetManager +
      +
    Probcons - Class in compbio.runner.msa
     
    Probcons() - +Constructor for class compbio.runner.msa.Probcons +
      +
    ProbconsWS - Class in compbio.ws.server
     
    ProbconsWS() - +Constructor for class compbio.ws.server.ProbconsWS +
      +
    PROC_ERR_FILE - +Static variable in class compbio.engine.local.ExecutableWrapper +
      +
    PROC_OUT_FILE - +Static variable in class compbio.engine.local.ExecutableWrapper +
      +
    Program - Enum in compbio.data.sequence
    Programmes that can produce alignments
    ProgressGetter - Class in compbio.engine
     
    ProgressGetter() - +Constructor for class compbio.engine.ProgressGetter +
      +
    PropertyHelperManager - Class in compbio.engine.conf
     
    PropertyHelperManager() - +Constructor for class compbio.engine.conf.PropertyHelperManager +
      +
    PScore - Class in compbio.pipeline._jpred
     
    PScore() - +Constructor for class compbio.pipeline._jpred.PScore +
      +
    PSIBlast - Class in compbio.runner._impl
     
    PSIBlast(String) - +Constructor for class compbio.runner._impl.PSIBlast +
      +
    PsiBlast - Class in compbio.runner.psiblast
     
    PsiBlast() - +Constructor for class compbio.runner.psiblast.PsiBlast +
      +
    pull(long) - +Method in class compbio.engine.FilePuller +
      +
    pull(String, long) - +Static method in class compbio.engine.ProgressGetter +
      +
    PulledFileCache - Class in compbio.engine
     
    PulledFileCache() - +Constructor for class compbio.engine.PulledFileCache +
      +
    PullExecStatistics - Class in compbio.data.msa.jaxws
     
    PullExecStatistics() - +Constructor for class compbio.data.msa.jaxws.PullExecStatistics +
      +
    pullExecStatistics(String, long) - +Method in interface compbio.data.msa.MsaWS +
    Reads 1kb chunk from the statistics file which is specific to a given web + service from the position. +
    pullExecStatistics(String, long) - +Method in class compbio.ws.server.ClustalWS +
      +
    pullExecStatistics(String, long) - +Method in class compbio.ws.server.MafftWS +
      +
    pullExecStatistics(String, long) - +Method in class compbio.ws.server.MuscleWS +
      +
    pullExecStatistics(String, long) - +Method in class compbio.ws.server.ProbconsWS +
      +
    pullExecStatistics(String, long) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
     
    PullExecStatisticsResponse() - +Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse +
      +
    PullFile - Class in compbio.data.msa.jaxws
     
    PullFile() - +Constructor for class compbio.data.msa.jaxws.PullFile +
      +
    pullFile(String, long) - +Static method in class compbio.ws.server.WSUtil +
      +
    PullFileResponse - Class in compbio.data.msa.jaxws
     
    PullFileResponse() - +Constructor for class compbio.data.msa.jaxws.PullFileResponse +
      +
    put(FilePuller) - +Static method in class compbio.engine.PulledFileCache +
    This method allows duplicates to be added. +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
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    +R

    +
    +
    rconfigFile - +Static variable in class compbio.engine.client.RunConfiguration +
      +
    read(InputStream, Class<V>) - +Method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    read(InputStream, Class<V>, Class<?>...) - +Method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    readAndValidate(InputStream, Class<V>) - +Method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    readClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Read Clustal formatted alignment. +
    readClustalFile(File) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    readClustalFile(String, String) - +Static method in class compbio.runner.Util +
      +
    readFasta(InputStream) - +Static method in class compbio.data.sequence.SequenceUtil +
    Reads fasta sequences from inStream into the list of FastaSequence + objects +
    removeArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument Argument if found. +
    removeArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Removes the argument +
    removeJob(String) - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    removeOutput(String) - +Method in class compbio.runner._impl.BlastAll +
      +
    removeOutput(String) - +Method in class compbio.runner._impl.PSIBlast +
      +
    removeParam(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    removeTask(ConfiguredExecutable<?>) - +Static method in class compbio.engine.SubmissionManager +
      +
    removeTask(String) - +Static method in class compbio.engine.SubmissionManager +
      +
    ResultNotAvailableException - Exception in compbio.metadata
    ResultNotAvailableException is thrown wherever the results of the calculation + cannot be obtained.
    ResultNotAvailableException(String) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableException(String, Throwable) - +Constructor for exception compbio.metadata.ResultNotAvailableException +
      +
    ResultNotAvailableExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    ResultNotAvailableExceptionBean() - +Constructor for class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean +
      +
    Ronn - Class in compbio.runner._impl
     
    Ronn(String) - +Constructor for class compbio.runner._impl.Ronn +
      +
    RPSBlast - Class in compbio.runner._impl
     
    RPSBlast(String) - +Constructor for class compbio.runner._impl.RPSBlast +
      +
    run() - +Method in class compbio.engine.local.StreamGobbler +
      +
    RunConfiguration - Class in compbio.engine.client
    Value class for persisting ConfExecutable instances
    RunConfiguration() - +Constructor for class compbio.engine.client.RunConfiguration +
      +
    RunConfiguration(ConfExecutable<?>) - +Constructor for class compbio.engine.client.RunConfiguration +
      +
    RunnerConfig<T> - Class in compbio.metadata
    The list of Parameters and Options supported by executable.
    RunnerConfig() - +Constructor for class compbio.metadata.RunnerConfig +
      +
    RunnerConfigMarshaller<T> - Class in compbio.engine.conf
     
    RunnerConfigMarshaller(Class<?>) - +Constructor for class compbio.engine.conf.RunnerConfigMarshaller +
      +
    RunnerConfigMarshaller(Class<?>, Class<?>...) - +Constructor for class compbio.engine.conf.RunnerConfigMarshaller +
      +
    Runners - Class in compbio.runner._impl
     
    runPsiBlast() - +Method in class compbio.pipeline._jpred.Jpred4 +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
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    +

    +S

    +
    +
    saveRunConfiguration() - +Method in class compbio.engine.client.ConfExecutable +
      +
    saveRunConfiguration() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    SequenceUtil - Class in compbio.data.sequence
    Utility class for operations on sequences
    setActualNumberofSequences(int) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    setDefaultValue(String) - +Method in class compbio.metadata.Option +
    Sets one of the values defined in optionList as default. +
    setDefaultValue(String) - +Method in class compbio.metadata.Parameter +
      +
    setDescription(String) - +Method in class compbio.metadata.Option +
      +
    setDescription(String) - +Method in class compbio.metadata.Preset +
      +
    setEmail(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    setError(String) - +Method in class compbio.engine.client.RunConfiguration +
      +
    setError(String) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    setExecProvider(Executable.ExecProvider) - +Method in class compbio.engine.client.ConfExecutable +
      +
    setFastaSequences(List<FastaSequence>) - +Method in class compbio.data.msa.jaxws.Align +
      +
    setFastaSequences(List<FastaSequence>) - +Method in class compbio.data.msa.jaxws.CustomAlign +
      +
    setFastaSequences(List<FastaSequence>) - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    setFirst(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setFurtherDetails(URL) - +Method in class compbio.metadata.Option +
      +
    setInput(String) - +Method in class compbio.engine.client.RunConfiguration +
      +
    setInput(String) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    setInput(String) - +Method in class compbio.runner.msa.ClustalW +
      +
    setInput(String) - +Method in class compbio.runner.msa.Mafft +
      +
    setInput(String) - +Method in class compbio.runner.msa.Muscle +
      +
    setInput(String) - +Method in class compbio.runner.msa.Probcons +
      +
    setInput(String) - +Method in class compbio.runner.msa.Tcoffee +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.CancelJob +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.GetJobStatus +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.GetProgress +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.GetResult +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    setJobId(String) - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    setLast(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setLast(String, String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setMax(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.JobExecutionExceptionBean +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean +
      +
    setMessage(String) - +Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean +
      +
    setMin(String) - +Method in class compbio.metadata.ValueConstrain +
      +
    setName(String) - +Method in class compbio.metadata.Option +
      +
    setName(String) - +Method in class compbio.metadata.Preset +
      +
    setName(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    setNCore(int) - +Method in class compbio.runner.msa.Tcoffee +
      +
    setNumberOfSequencesAllowed(int) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    setOptionName(String) - +Method in class compbio.metadata.Parameter +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Option +
      +
    setOptionNames(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setOptions(List<Option>) - +Method in class compbio.data.msa.jaxws.CustomAlign +
      +
    setOptions(List<String>) - +Method in class compbio.metadata.Preset +
      +
    setOptions(List<Option<T>>) - +Method in class compbio.metadata.RunnerConfig +
      +
    setOutput(String) - +Method in class compbio.engine.client.RunConfiguration +
      +
    setOutput(String) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    setOutput(String) - +Method in class compbio.runner.msa.ClustalW +
      +
    setOutput(String) - +Method in class compbio.runner.msa.Muscle +
      +
    setParam(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setParam(String, String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setParameter(String) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    setParameters(CommandBuilder<?>) - +Method in class compbio.engine.client.RunConfiguration +
      +
    setParameters(List<Parameter<T>>) - +Method in class compbio.metadata.RunnerConfig +
      +
    setParams(List<String>) - +Method in class compbio.engine.client.CommandBuilder +
      +
    setPosition(long) - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    setPosition(long) - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    setPossibleValues(Set<String>) - +Method in class compbio.metadata.Parameter +
      +
    setPreset(Preset) - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    setPresetName(String) - +Method in class compbio.data.msa.jaxws.GetLimit +
      +
    setPresets(List<Preset<T>>) - +Method in class compbio.metadata.PresetManager +
      +
    setPrmSeparator(String) - +Method in class compbio.metadata.RunnerConfig +
      +
    setQueue(String) - +Method in class compbio.runner._NativeSpecHelper +
      +
    setRequired(boolean) - +Method in class compbio.metadata.Option +
      +
    setRequiredMemory(int) - +Method in class compbio.runner._NativeSpecHelper +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.AlignResponse +
      +
    setReturn(boolean) - +Method in class compbio.data.msa.jaxws.CancelJobResponse +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.CustomAlignResponse +
      +
    setReturn(JobStatus) - +Method in class compbio.data.msa.jaxws.GetJobStatusResponse +
      +
    setReturn(Limit) - +Method in class compbio.data.msa.jaxws.GetLimitResponse +
      +
    setReturn(LimitsManager) - +Method in class compbio.data.msa.jaxws.GetLimitsResponse +
      +
    setReturn(PresetManager) - +Method in class compbio.data.msa.jaxws.GetPresetsResponse +
      +
    setReturn(byte) - +Method in class compbio.data.msa.jaxws.GetProgressResponse +
      +
    setReturn(Alignment) - +Method in class compbio.data.msa.jaxws.GetResultResponse +
      +
    setReturn(RunnerConfig) - +Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse +
      +
    setReturn(String) - +Method in class compbio.data.msa.jaxws.PresetAlignResponse +
      +
    setReturn(ChunkHolder) - +Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse +
      +
    setReturn(ChunkHolder) - +Method in class compbio.data.msa.jaxws.PullFileResponse +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.PresetManager +
      +
    setRunnerClassName(String) - +Method in class compbio.metadata.RunnerConfig +
      +
    setSequenceLenghtActual(int) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    setSequenceLenghtAllowed(int) - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    setType(ValueConstrain.Type) - +Method in class compbio.metadata.ValueConstrain +
      +
    setValidValue(ValueConstrain) - +Method in class compbio.metadata.Parameter +
      +
    setValue(String) - +Method in interface compbio.metadata.Argument +
    Set default values for the parameter or an option +
    setValue(String) - +Method in class compbio.metadata.Option +
      +
    setWorkDirectory(String) - +Method in class compbio.engine.client.ConfExecutable +
      +
    setWorkDirectory(String) - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    SHORT_TIME_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    shutdown() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    shutDown() - +Static method in class compbio.engine.local.LocalExecutorService +
    This stops all executing processes via interruption. +
    shutdownNow() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    SimpleWSPublisher - Class in compbio.ws.server
    This class publish a web service.
    SimpleWSPublisher(Object, String) - +Constructor for class compbio.ws.server.SimpleWSPublisher +
      +
    size() - +Method in class compbio.engine.client.CommandBuilder +
      +
    SkeletalExecutable<T> - Class in compbio.engine.client
     
    SkeletalExecutable() - +Constructor for class compbio.engine.client.SkeletalExecutable +
      +
    SkeletalExecutable(String) - +Constructor for class compbio.engine.client.SkeletalExecutable +
      +
    SPACE - +Static variable in class compbio.runner.Util +
      +
    StatisticManager - Class in compbio.engine.cluster.drmaa
     
    StatisticManager(JobInfo) - +Constructor for class compbio.engine.cluster.drmaa.StatisticManager +
      +
    StreamGobbler - Class in compbio.engine.local
     
    SubmissionManager - Class in compbio.engine
    Submit jobs for execution
    submit(Callable<T>) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    submitJob(ConfiguredExecutable<?>) - +Method in interface compbio.engine.AsyncExecutor +
    Submits job for the execution + Immediate execution is not guaranteed, this method puts the job in the queue. +
    submitJob(ConfiguredExecutable<?>) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    submitJob(ConfiguredExecutable<?>) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    SyncExecutor - Interface in compbio.engine
    Synchronous executor, is an engine to run the Executable synchronously.
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +T

    +
    +
    Tcoffee - Class in compbio.runner.msa
     
    Tcoffee() - +Constructor for class compbio.runner.msa.Tcoffee +
      +
    TcoffeeWS - Class in compbio.ws.server
     
    TcoffeeWS() - +Constructor for class compbio.ws.server.TcoffeeWS +
      +
    termSignal() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    toCommand(String) - +Method in class compbio.metadata.Option +
    Convert the option to the command string. +
    toCommand(String) - +Method in class compbio.metadata.Parameter +
      +
    toString() - +Method in class compbio.data.sequence.Alignment +
      +
    toString() - +Method in class compbio.data.sequence.FastaSequence +
    Same as oneLineFasta +
    toString() - +Method in class compbio.engine.client.CommandBuilder +
      +
    toString() - +Method in class compbio.engine.client.ConfExecutable +
      +
    toString() - +Method in class compbio.engine.client.RunConfiguration +
      +
    toString() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    toString() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    toString() - +Method in enum compbio.engine.cluster.dundee._Queue +
      +
    toString() - +Method in class compbio.engine.conf._Key +
      +
    toString() - +Method in class compbio.engine.FilePuller +
      +
    toString() - +Method in class compbio.engine.Job +
      +
    toString() - +Method in class compbio.metadata.ChunkHolder +
      +
    toString() - +Method in class compbio.metadata.Limit +
      +
    toString() - +Method in class compbio.metadata.LimitsManager +
      +
    toString() - +Method in class compbio.metadata.Option +
      +
    toString() - +Method in class compbio.metadata.Parameter +
      +
    toString() - +Method in class compbio.metadata.Preset +
      +
    toString() - +Method in class compbio.metadata.PresetManager +
      +
    toString() - +Method in class compbio.metadata.RunnerConfig +
      +
    toString() - +Method in class compbio.metadata.ValueConstrain +
      +
    toString() - +Method in class compbio.pipeline._jpred.PScore +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +B

    +
    +
    BlastAll - Class in compbio.runner._impl
     
    BlastAll(String) - +Constructor for class compbio.runner._impl.BlastAll +
      +
    BlastParameters - Class in compbio.runner._impl
    Utility class for common Blast parameters
    BlastParser - Class in compbio.pipeline._jpred
     
    BlastParser() - +Constructor for class compbio.pipeline._jpred.BlastParser +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +
    UnknownFileFormatException - Exception in compbio.data.sequence
     
    UnknownFileFormatException() - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(File, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String, Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(String) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnknownFileFormatException(Throwable) - +Constructor for exception compbio.data.sequence.UnknownFileFormatException +
      +
    UnsupportedRuntimeException - Exception in compbio.metadata
    Indicates that the server could not execute native executables.
    UnsupportedRuntimeException(String) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    UnsupportedRuntimeException(Throwable) - +Constructor for exception compbio.metadata.UnsupportedRuntimeException +
      +
    UnsupportedRuntimeExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    UnsupportedRuntimeExceptionBean() - +Constructor for class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean +
      +
    Util - Class in compbio.engine.client
     
    Util() - +Constructor for class compbio.engine.client.Util +
      +
    Util - Class in compbio.runner
     
    Util() - +Constructor for class compbio.runner.Util +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +V

    +
    +
    validate(Validator, String) - +Static method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    validate(PresetManager<T>) - +Method in class compbio.metadata.LimitsManager +
    Validate Limits +
    validate(RunnerConfig<T>) - +Method in class compbio.metadata.PresetManager +
    Checks whether preset option and parameter are defined in RunnerConfig + object. +
    validate() - +Method in class compbio.metadata.RunnerConfig +
    Validate the arguments +
    validateDirectory(String) - +Static method in class compbio.engine.client.PathValidator +
      +
    validateExecutable(String) - +Static method in class compbio.engine.client.PathValidator +
      +
    validateFastaInput(List<FastaSequence>) - +Static method in class compbio.ws.server.WSUtil +
      +
    validateJobId(String) - +Static method in class compbio.ws.server.WSUtil +
      +
    validatePathNames(List<String>, String) - +Static method in class compbio.engine.client.PathValidator +
      +
    validURL(String) - +Static method in class compbio.ws.client.Jws2Client +
    Attempt to construct the URL object from the string +
    ValueConstrain - Class in compbio.metadata
    The type and the lower and upper boundaries for numerical value.
    ValueConstrain() - +Constructor for class compbio.metadata.ValueConstrain +
      +
    ValueConstrain.Type - Enum in compbio.metadata
     
    valueOf(String) - +Static method in enum compbio.data._structure.JnetAnnotation +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.data._structure.JpredAnnotation +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.data.sequence.Program +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.engine.client.Executable.ExecProvider +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.engine.cluster.dundee._Queue +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.JobStatus +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns the enum constant of this type with the specified name. +
    valueOf(String) - +Static method in enum compbio.ws.client.Jws2Client.Services +
    Returns the enum constant of this type with the specified name. +
    values() - +Static method in enum compbio.data._structure.JnetAnnotation +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.data._structure.JpredAnnotation +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.data.sequence.Program +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.engine.client.Executable.ExecProvider +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.engine.cluster.dundee._Queue +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.JobStatus +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.metadata.ValueConstrain.Type +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    values() - +Static method in enum compbio.ws.client.Jws2Client.Services +
    Returns an array containing the constants of this enum type, in +the order they are declared. +
    +
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    +W

    +
    +
    waitForFile(long) - +Method in class compbio.engine.FilePuller +
      +
    waitForJob(String) - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    waitForJob(String, long) - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    waitForResult(ClusterSession, String) - +Static method in class compbio.engine.cluster.drmaa.ClusterUtil +
      +
    waitForResult() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    waitForResult() - +Method in class compbio.engine.local.LocalRunner +
      +
    waitForResult() - +Method in interface compbio.engine.SyncExecutor +
    Call to this method block for as long as it is required for an executable to finish its job. +
    wasAborted() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    WHITE_SPACE - +Static variable in class compbio.data.sequence.SequenceUtil +
    A whitespace character: [\t\n\x0B\f\r] +
    write(RunConfiguration) - +Static method in class compbio.engine.client.RunConfiguration +
      +
    write(Object, OutputStream) - +Method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    writeAndValidate(Object, String, OutputStream) - +Method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    writeClustalAlignment(OutputStream, Alignment) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
    Write Clustal formatted alignment Limitations: does not record the + consensus. +
    writeFasta(OutputStream, List<FastaSequence>, int) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes list of FastaSequeces into the outstream formatting the sequence + so that it contains width chars on each line +
    writeFasta(OutputStream, List<FastaSequence>) - +Static method in class compbio.data.sequence.SequenceUtil +
    Writes FastaSequence in the file, each sequence will take one line only +
    writeFile(String, String, String, boolean) - +Static method in class compbio.engine.client.Util +
      +
    writeInput(List<FastaSequence>, ConfiguredExecutable<?>) - +Static method in class compbio.runner.Util +
      +
    writeMarker(String, JobStatus) - +Static method in class compbio.engine.client.Util +
      +
    writeStatFile(String, String) - +Static method in class compbio.engine.client.Util +
      +
    WrongParameterException - Exception in compbio.metadata
    WrongParameterException is thrown wherever the RunnerConfig object + does not match the actual runnable or then attempting to set the value of + Argument to invalid value.
    WrongParameterException(Option<?>) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterException(String, Throwable) - +Constructor for exception compbio.metadata.WrongParameterException +
      +
    WrongParameterExceptionBean - Class in compbio.data.msa.jaxws
    This class was generated by the JAX-WS RI.
    WrongParameterExceptionBean() - +Constructor for class compbio.data.msa.jaxws.WrongParameterExceptionBean +
      +
    WSTester - Class in compbio.ws.client
    Class for testing web services
    WSTester() - +Constructor for class compbio.ws.client.WSTester +
      +
    WSUtil - Class in compbio.ws.server
     
    WSUtil() - +Constructor for class compbio.ws.server.WSUtil +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +
    +
    _DrmaaExample - Class in compbio.engine.cluster.drmaa
     
    _DrmaaExample() - +Constructor for class compbio.engine.cluster.drmaa._DrmaaExample +
      +
    _JobStatus - Class in compbio.engine.cluster.drmaa
     
    _JobStatus() - +Constructor for class compbio.engine.cluster.drmaa._JobStatus +
      +
    _Jpred - Class in compbio.runner._jpred
     
    _Jpred() - +Constructor for class compbio.runner._jpred._Jpred +
      +
    _Key - Class in compbio.engine.conf
     
    _Key(Class<?>) - +Constructor for class compbio.engine.conf._Key +
      +
    _NativeSpecHelper - Class in compbio.runner
     
    _NativeSpecHelper(int) - +Constructor for class compbio.runner._NativeSpecHelper +
      +
    _NativeSpecHelper(int, int) - +Constructor for class compbio.runner._NativeSpecHelper +
      +
    _Queue - Enum in compbio.engine.cluster.dundee
     
    _QueueConstraints - Class in compbio.engine.cluster.dundee
     
    _SkeletalCommandBuilder - Class in compbio.runner
     
    _SkeletalCommandBuilder() - +Constructor for class compbio.runner._SkeletalCommandBuilder +
      +
    _TrackingExecutor - Class in compbio.engine.local
    This executor extends standard Java ExecutorService by adding the method to + obtain all Runnables which were running and did not complete upon executor + termination.
    _TrackingExecutor(ExecutorService) - +Constructor for class compbio.engine.local._TrackingExecutor +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + + + + + + + + + + + + + +
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    +C

    +
    +
    call() - +Method in class compbio.engine.local.ExecutableWrapper +
    It is vital that output and error streams are captured immediately for + this call() to succeed. +
    canAcceptMoreWork() - +Method in class compbio.engine.local.LocalExecutorService +
    If the Executor queue is empty +
    CancelJob - Class in compbio.data.msa.jaxws
     
    CancelJob() - +Constructor for class compbio.data.msa.jaxws.CancelJob +
      +
    cancelJob(String) - +Method in interface compbio.data.msa.MsaWS +
    Stop running job but leave its output untouched +
    cancelJob(String) - +Method in interface compbio.engine.AsyncExecutor +
    Stop running job. +
    cancelJob(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    cancelJob(String, ClusterSession) - +Static method in class compbio.engine.cluster.drmaa.ClusterUtil +
      +
    cancelJob() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    cancelJob(String) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    cancelJob(Future<ConfiguredExecutable<?>>, String) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    cancelJob() - +Method in class compbio.engine.local.LocalRunner +
      +
    cancelJob() - +Method in interface compbio.engine.SyncExecutor +
    Stops running job. +
    cancelJob(String) - +Method in class compbio.ws.server.ClustalWS +
      +
    cancelJob(String) - +Method in class compbio.ws.server.MafftWS +
      +
    cancelJob(String) - +Method in class compbio.ws.server.MuscleWS +
      +
    cancelJob(String) - +Method in class compbio.ws.server.ProbconsWS +
      +
    cancelJob(String) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    cancelJob(String) - +Static method in class compbio.ws.server.WSUtil +
      +
    CancelJobResponse - Class in compbio.data.msa.jaxws
     
    CancelJobResponse() - +Constructor for class compbio.data.msa.jaxws.CancelJobResponse +
      +
    ChunkHolder - Class in compbio.metadata
    Represents a chunk of string data together with the position in a file from + where corresponding to of the data.
    ChunkHolder(String, long) - +Constructor for class compbio.metadata.ChunkHolder +
      +
    Cleaner - Class in compbio.engine
     
    Cleaner() - +Constructor for class compbio.engine.Cleaner +
      +
    cleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all whitespace chars in the sequence string +
    cleanup(String) - +Method in interface compbio.engine.AsyncExecutor +
    Remove all files and a job directory for a jobid. +
    cleanup(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    cleanup() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    cleanup(String) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    cleanup(ConfiguredExecutable<?>) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    cleanup() - +Method in class compbio.engine.local.LocalRunner +
      +
    cleanup() - +Method in interface compbio.engine.SyncExecutor +
    Clean up after the job +
    close() - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    ClustalAlignmentUtil - Class in compbio.data.sequence
    Tools to read and write clustal formated files
    ClustalAlignmentUtil() - +Constructor for class compbio.data.sequence.ClustalAlignmentUtil +
      +
    ClustalW - Class in compbio.runner.msa
     
    ClustalW() - +Constructor for class compbio.runner.msa.ClustalW +
      +
    ClustalWS - Class in compbio.ws.server
     
    ClustalWS() - +Constructor for class compbio.ws.server.ClustalWS +
      +
    CLUSTER_STAT_IN_SEC - +Static variable in class compbio.engine.cluster.drmaa.ClusterUtil +
      +
    CLUSTER_TASK_ID_PREFIX - +Static variable in class compbio.engine.client.ConfExecutable +
      +
    CLUSTER_WORK_DIRECTORY - +Static variable in class compbio.engine.Configurator +
      +
    ClusterJobId - Class in compbio.engine
     
    ClusterJobId(String) - +Constructor for class compbio.engine.ClusterJobId +
      +
    ClusterNativeSpecExecutable<T> - Interface in compbio.engine.client
     
    ClusterSession - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil - Class in compbio.engine.cluster.drmaa
     
    ClusterUtil() - +Constructor for class compbio.engine.cluster.drmaa.ClusterUtil +
      +
    CommandBuilder<T> - Class in compbio.engine.client
     
    CommandBuilder(String) - +Constructor for class compbio.engine.client.CommandBuilder +
      +
    compareTo(Delayed) - +Method in class compbio.engine.FilePuller +
      +
    compbio.data._structure - package compbio.data._structure
     
    compbio.data.msa - package compbio.data.msa
     
    compbio.data.msa.jaxws - package compbio.data.msa.jaxws
     
    compbio.pipeline._jpred - package compbio.pipeline._jpred
     
    compbio.runner._jpred - package compbio.runner._jpred
     
    compbio.runner.psiblast - package compbio.runner.psiblast
     
    compbio.ws.client - package compbio.ws.client
     
    compbio.ws.server - package compbio.ws.server
     
    confDir - +Static variable in class compbio.engine.conf.PropertyHelperManager +
      +
    ConfExecutable<T> - Class in compbio.engine.client
     
    ConfExecutable(Executable<T>, String) - +Constructor for class compbio.engine.client.ConfExecutable +
      +
    Configurator - Class in compbio.engine
     
    Configurator() - +Constructor for class compbio.engine.Configurator +
      +
    ConfiguredExecutable<T> - Interface in compbio.engine.client
     
    configureExecutable(Executable<T>) - +Static method in class compbio.engine.Configurator +
      +
    configureExecutable(Executable<T>, List<FastaSequence>) - +Static method in class compbio.engine.Configurator +
      +
    configureExecutable(Executable<T>, Executable.ExecProvider) - +Static method in class compbio.engine.Configurator +
      +
    connect(String, Jws2Client.Services) - +Static method in class compbio.ws.client.Jws2Client +
    Connects to a web service by the host and the service name +
    convertToAbsolute(String) - +Static method in class compbio.engine.client.Util +
      +
    copyAndValidateRConfig(RunnerConfig<?>) - +Method in class compbio.metadata.RunnerConfig +
      +
    countMatchesInSequence(String, String) - +Static method in class compbio.data.sequence.FastaSequence +
      +
    CustomAlign - Class in compbio.data.msa.jaxws
     
    CustomAlign() - +Constructor for class compbio.data.msa.jaxws.CustomAlign +
      +
    customAlign(List<FastaSequence>, List<Option<T>>) - +Method in interface compbio.data.msa.MsaWS +
    Align a list of sequences with options. +
    customAlign(List<FastaSequence>, List<Option<ClustalW>>) - +Method in class compbio.ws.server.ClustalWS +
      +
    customAlign(List<FastaSequence>, List<Option<Mafft>>) - +Method in class compbio.ws.server.MafftWS +
      +
    customAlign(List<FastaSequence>, List<Option<Muscle>>) - +Method in class compbio.ws.server.MuscleWS +
      +
    customAlign(List<FastaSequence>, List<Option<Probcons>>) - +Method in class compbio.ws.server.ProbconsWS +
      +
    customAlign(List<FastaSequence>, List<Option<Tcoffee>>) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    CustomAlignResponse - Class in compbio.data.msa.jaxws
     
    CustomAlignResponse() - +Constructor for class compbio.data.msa.jaxws.CustomAlignResponse +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +D

    +
    +
    deepClean() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    deepCleanSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Removes all special characters and digits as well as whitespace chars + from the sequence +
    deleteAllFiles(String) - +Static method in class compbio.engine.Cleaner +
      +
    deleteFiles(ConfiguredExecutable<?>) - +Static method in class compbio.engine.Cleaner +
    This method returns true if all files specified by List files were + successfully removed or there was no files to remove (files list was + empty) +
    DELIM - +Static variable in class compbio.engine.conf._Key +
      +
    DELIM - +Static variable in class compbio.engine.conf.DirectoryManager +
      +
    DIGIT - +Static variable in class compbio.data.sequence.SequenceUtil +
    A digit +
    DirectoryManager - Class in compbio.engine.conf
     
    DirectoryManager() - +Constructor for class compbio.engine.conf.DirectoryManager +
      +
    disconnect() - +Method in class compbio.engine.FilePuller +
      +
    Disembl - Class in compbio.runner._impl
     
    Disembl(String) - +Constructor for class compbio.runner._impl.Disembl +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    + + + diff --git a/website/full_javadoc/index-files/index-5.html b/website/full_javadoc/index-files/index-5.html new file mode 100644 index 0000000..46a4b47 --- /dev/null +++ b/website/full_javadoc/index-files/index-5.html @@ -0,0 +1,215 @@ + + + + + + +E-Index + + + + + + + + + + + + +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    +E

    +
    +
    Environment - Class in compbio.runner._impl
    This is utility class to encapsulate environmental variables like directory paths
    EnvVariableProcessor - Class in compbio.engine.client
     
    EnvVariableProcessor() - +Constructor for class compbio.engine.client.EnvVariableProcessor +
      +
    equals(Object) - +Method in class compbio.data.sequence.Alignment +
    Please note that this implementation does not take the order of sequences + into account! +
    equals(Object) - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    equals(Object) - +Method in class compbio.data.sequence.FastaSequence +
      +
    equals(Object) - +Method in class compbio.engine.client.CommandBuilder +
      +
    equals(Object) - +Method in class compbio.engine.client.RunConfiguration +
      +
    equals(Object) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    equals(Object) - +Method in class compbio.engine.ClusterJobId +
      +
    equals(Object) - +Method in class compbio.engine.conf._Key +
      +
    equals(Object) - +Method in class compbio.engine.FilePuller +
      +
    equals(Object) - +Method in class compbio.engine.Job +
      +
    equals(Object) - +Method in class compbio.metadata.ChunkHolder +
      +
    equals(Object) - +Method in class compbio.metadata.Limit +
      +
    equals(Object) - +Method in class compbio.metadata.Option +
      +
    equals(Object) - +Method in class compbio.metadata.Parameter +
      +
    equals(Object) - +Method in class compbio.metadata.Preset +
      +
    equals(Object) - +Method in class compbio.metadata.RunnerConfig +
      +
    equals(Object) - +Method in class compbio.metadata.ValueConstrain +
      +
    equals(Object) - +Method in class compbio.pipeline._jpred.PScore +
      +
    Executable<T> - Interface in compbio.engine.client
    Interface to a native executable.
    Executable.ExecProvider - Enum in compbio.engine.client
     
    ExecutableWrapper - Class in compbio.engine.local
     
    ExecutableWrapper(ConfiguredExecutable<?>, String) - +Constructor for class compbio.engine.local.ExecutableWrapper +
      +
    execute(Runnable) - +Method in class compbio.engine.local._TrackingExecutor +
      +
    executeJob() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    executeJob() - +Method in class compbio.engine.local.LocalRunner +
      +
    executeJob() - +Method in interface compbio.engine.SyncExecutor +
    Execute the job +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    +

    +F

    +
    +
    FastaSequence - Class in compbio.data.sequence
    A FASTA formatted sequence.
    FastaSequence(String, String) - +Constructor for class compbio.data.sequence.FastaSequence +
    Upon construction the any whitespace characters are removed from the + sequence +
    FilePuller - Class in compbio.engine
     
    FIRST_MEMORY_LIMIT - +Static variable in class compbio.engine.cluster.dundee._QueueConstraints +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
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    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
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    + + + +A B C D E F G H I J K L M N O P R S T U V W _
    +

    +G

    +
    +
    gapchar - +Static variable in class compbio.data.sequence.ClustalAlignmentUtil +
    Dash char to be used as gap char in the alignments +
    get(String) - +Static method in class compbio.engine.PulledFileCache +
      +
    getActualNumberofSequences() - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    getActualNumberofSequences() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getAllConstrainedParametersWithBorderValues(boolean) - +Method in class compbio.runner.OptionCombinator +
      +
    getAllConstrainedParametersWithRandomValues() - +Method in class compbio.runner.OptionCombinator +
      +
    getAllOptions() - +Method in class compbio.runner.OptionCombinator +
      +
    getAllParameters() - +Method in class compbio.runner.OptionCombinator +
      +
    getAllStats() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getApproprieteQueue() - +Method in class compbio.runner._NativeSpecHelper +
      +
    getArgument(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by its name if found, NULL otherwise +
    getArgumentByOptionName(String) - +Method in class compbio.metadata.RunnerConfig +
    Returns the argument by option name, NULL if the argument is not found +
    getArguments(RunnerConfig<T>) - +Method in class compbio.metadata.Preset +
    Converts list of options as String to type Option +
    getArguments() - +Method in class compbio.metadata.RunnerConfig +
      +
    getAsyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - +Static method in class compbio.engine.Configurator +
      +
    getAsyncEngine(ConfiguredExecutable<?>) - +Static method in class compbio.engine.Configurator +
      +
    getAsyncEngine(String) - +Static method in class compbio.engine.Configurator +
      +
    getAvgSeqLength() - +Method in class compbio.metadata.Limit +
      +
    getAvgSequenceLength(List<FastaSequence>) - +Static method in class compbio.metadata.Limit +
    Calculates an average sequence length of the dataset +
    getBlastAllRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getBlastBinDir() - +Static method in class compbio.runner._impl.Environment +
      +
    getBlastDatabasesDir() - +Static method in class compbio.runner._impl.Environment +
      +
    getByJobId(String, List<Job>) - +Static method in class compbio.engine.Job +
      +
    getByTaskId(String, List<Job>) - +Static method in class compbio.engine.Job +
      +
    getCalculationTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getCancelledTasks() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    getChunk() - +Method in class compbio.metadata.ChunkHolder +
      +
    getClass(String) - +Static method in class compbio.engine.conf.DirectoryManager +
      +
    getClusterCpuNum() - +Static method in class compbio.runner.msa.Tcoffee +
      +
    getClusterJobId(String) - +Static method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getClusterSettings() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.engine.client.ConfExecutable +
      +
    getCommand(Executable.ExecProvider) - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getCommand(Executable.ExecProvider, Class<?>) - +Static method in class compbio.engine.client.Util +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.BlastAll +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.Disembl +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.Mcl +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.PSIBlast +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.Ronn +
      +
    getCommand(Executable.ExecProvider) - +Method in class compbio.runner._impl.RPSBlast +
      +
    getCommandName() - +Method in class compbio.runner._impl.BlastAll +
      +
    getCommandName() - +Method in class compbio.runner._impl.Disembl +
      +
    getCommandName() - +Method in class compbio.runner._impl.Mcl +
      +
    getCommandName() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getCommandName() - +Method in class compbio.runner._impl.PSIBlast +
      +
    getCommandName() - +Method in class compbio.runner._impl.Ronn +
      +
    getCommandName() - +Static method in class compbio.runner._impl.RPSBlast +
      +
    getCommands() - +Method in class compbio.engine.client.CommandBuilder +
      +
    getCommands(List<Option<T>>, String) - +Static method in class compbio.ws.server.WSUtil +
      +
    getCommandString() - +Method in class compbio.engine.client.CommandBuilder +
      +
    getConfExecutable() - +Method in class compbio.engine.Job +
      +
    getCPUTimeStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getCPUUsageTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getCreatedFiles() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getCreatedFiles() - +Method in interface compbio.engine.client.Executable +
      +
    getCreatedFiles() - +Method in class compbio.engine.client.SkeletalExecutable +
    This method cannot really tell whether the files has actually been + created or not. +
    getCreatedFiles() - +Method in class compbio.runner._impl.BlastAll +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.Disembl +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.Mcl +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.OB +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.PSIBlast +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.Ronn +
      +
    getCreatedFiles() - +Method in class compbio.runner._impl.RPSBlast +
      +
    getCreatedFiles() - +Method in class compbio.runner.msa.ClustalW +
      +
    getCreatedFiles() - +Method in class compbio.runner.msa.Muscle +
      +
    getCreatedFiles() - +Method in class compbio.runner.msa.Probcons +
      +
    getCreatedFiles() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getDataTransfered() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getDefaultLimit() - +Method in class compbio.metadata.LimitsManager +
      +
    getDefaultValue() - +Method in interface compbio.metadata.Argument +
      +
    getDefaultValue() - +Method in class compbio.metadata.Option +
    A default value of the option. +
    getDelay(TimeUnit) - +Method in class compbio.engine.FilePuller +
      +
    getDescription() - +Method in interface compbio.metadata.Argument +
      +
    getDescription() - +Method in class compbio.metadata.Option +
    A long description of the Option +
    getDescription() - +Method in class compbio.metadata.Preset +
      +
    getDisemblRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getEmail() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getEndTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getEngine(Executable<?>) - +Static method in class compbio.engine.LoadBalancer +
      +
    getEngine(Executable<V>, List<FastaSequence>) - +Static method in class compbio.engine.LoadBalancer +
      +
    getEngine(ConfiguredExecutable<?>) - +Static method in class compbio.ws.server.WSUtil +
      +
    getEnvironment() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getEnvironment() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getEnvVariables(String, Class<?>) - +Static method in class compbio.engine.client.EnvVariableProcessor +
      +
    getError() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getError() - +Method in interface compbio.engine.client.Executable +
      +
    getError() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getError() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getError() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getError() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getExecProperty(String, Executable<?>) - +Static method in class compbio.engine.client.Util +
      +
    getExecProperty(String, Class<?>) - +Static method in class compbio.engine.client.Util +
      +
    getExecProvider() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getExecProvider() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getExecutable() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getExecutable() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getExecutionStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getExecutor() - +Static method in class compbio.engine.local.LocalExecutorService +
    This method returns the single instance of CachedThreadPoolExecutor which + it cashes internally +
    getExitStatus() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.Align +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.CustomAlign +
      +
    getFastaSequences() - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    getFile() - +Method in class compbio.engine.FilePuller +
      +
    getFormatedSequence(int) - +Method in class compbio.data.sequence.FastaSequence +
    Format sequence per width letter in one string. +
    getFormattedFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getFullPath(String, String) - +Static method in class compbio.engine.client.Util +
      +
    getFurtherDetails() - +Method in interface compbio.metadata.Argument +
      +
    getFurtherDetails() - +Method in class compbio.metadata.Option +
    The URL where further details about the option can be found +
    getGapchar() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    getHost(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts host name from the command line +
    getId() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of id +
    getInput() - +Method in class compbio.engine.client.ConfExecutable +
    Not all input paths are relative! Input path could be absolute! +
    getInput() - +Method in interface compbio.engine.client.Executable +
      +
    getInput() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getInput() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getInput() - +Method in class compbio.runner._impl.BlastAll +
      +
    getInput() - +Method in class compbio.runner._impl.Disembl +
      +
    getInput() - +Method in class compbio.runner._impl.Mcl +
      +
    getInput() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getInput() - +Method in class compbio.runner._impl.OB +
      +
    getInput() - +Method in class compbio.runner._impl.PSIBlast +
      +
    getInput() - +Method in class compbio.runner._impl.Ronn +
      +
    getInput() - +Method in class compbio.runner._impl.RPSBlast +
      +
    getInstance(ConfiguredExecutable<?>) - +Static method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    getIOWait() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.CancelJob +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetJobStatus +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetProgress +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.GetResult +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    getJobId() - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    getJobId() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getJobId() - +Method in class compbio.engine.ClusterJobId +
      +
    getJobId() - +Method in class compbio.engine.Job +
      +
    getJobInfo() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
    This method will block before the calculation has completed and then + return the object containing a job execution statistics +
    getJobPriority() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    GetJobStatus - Class in compbio.data.msa.jaxws
     
    GetJobStatus() - +Constructor for class compbio.data.msa.jaxws.GetJobStatus +
      +
    getJobStatus(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the status of the job. +
    getJobStatus(String) - +Method in interface compbio.engine.AsyncExecutor +
    Query the status of the job +
    getJobStatus(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
    This will never return clust.engine.JobStatus.CANCELLED as for sun grid + engine cancelled job is the same as failed. +
    getJobStatus(ClusterJobId) - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
    Apparently completed jobs cannot be found! If this happened most likely + that the job is not running any more and Most likely it has been + cancelled, finished or failed. +
    getJobStatus(int) - +Static method in class compbio.engine.cluster.drmaa.ClusterSession +
    Deprecated.  +
    getJobStatus() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    getJobStatus(String) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    getJobStatus(Future<ConfiguredExecutable<?>>) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    getJobStatus() - +Method in class compbio.engine.local.LocalRunner +
      +
    getJobStatus() - +Method in interface compbio.engine.SyncExecutor +
    Query the status of the job by its id. +
    getJobStatus(String) - +Method in class compbio.ws.server.ClustalWS +
      +
    getJobStatus(String) - +Method in class compbio.ws.server.MafftWS +
      +
    getJobStatus(String) - +Method in class compbio.ws.server.MuscleWS +
      +
    getJobStatus(String) - +Method in class compbio.ws.server.ProbconsWS +
      +
    getJobStatus(String) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    getJobStatus(String) - +Static method in class compbio.ws.server.WSUtil +
      +
    GetJobStatusResponse - Class in compbio.data.msa.jaxws
     
    GetJobStatusResponse() - +Constructor for class compbio.data.msa.jaxws.GetJobStatusResponse +
      +
    getLength() - +Method in class compbio.data.sequence.FastaSequence +
      +
    GetLimit - Class in compbio.data.msa.jaxws
     
    GetLimit() - +Constructor for class compbio.data.msa.jaxws.GetLimit +
      +
    getLimit(String) - +Method in interface compbio.data.msa.MsaWS +
    Get a Limit for a preset. +
    getLimit(String) - +Method in class compbio.engine.client.ConfExecutable +
      +
    getLimit(String) - +Method in interface compbio.engine.client.Executable +
      +
    getLimit(String) - +Method in class compbio.runner._impl.NetNglyc +
      +
    getLimit(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getLimit(String) - +Method in class compbio.runner.msa.ClustalW +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Mafft +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Muscle +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Probcons +
      +
    getLimit(String) - +Method in class compbio.runner.msa.Tcoffee +
      +
    getLimit(String) - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getLimit(String) - +Method in class compbio.ws.server.ClustalWS +
      +
    getLimit(String) - +Method in class compbio.ws.server.MafftWS +
      +
    getLimit(String) - +Method in class compbio.ws.server.MuscleWS +
      +
    getLimit(String) - +Method in class compbio.ws.server.ProbconsWS +
      +
    getLimit(String) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    getLimitByName(String) - +Method in class compbio.metadata.LimitsManager +
      +
    GetLimitResponse - Class in compbio.data.msa.jaxws
     
    GetLimitResponse() - +Constructor for class compbio.data.msa.jaxws.GetLimitResponse +
      +
    GetLimits - Class in compbio.data.msa.jaxws
     
    GetLimits() - +Constructor for class compbio.data.msa.jaxws.GetLimits +
      +
    getLimits() - +Method in interface compbio.data.msa.MsaWS +
    List Limits supported by a web service. +
    getLimits() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getLimits() - +Method in interface compbio.engine.client.Executable +
      +
    getLimits() - +Method in class compbio.metadata.LimitsManager +
      +
    getLimits() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getLimits() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getLimits() - +Method in class compbio.runner.msa.ClustalW +
      +
    getLimits() - +Method in class compbio.runner.msa.Mafft +
      +
    getLimits() - +Method in class compbio.runner.msa.Muscle +
      +
    getLimits() - +Method in class compbio.runner.msa.Probcons +
      +
    getLimits() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getLimits() - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getLimits(Class<? extends Executable<T>>) - +Static method in class compbio.runner.Util +
    For now just assume that all parameters which came in needs setting it + will be a client responsibility to prepare RunnerConfig object then +
    getLimits() - +Method in class compbio.ws.server.ClustalWS +
      +
    getLimits() - +Method in class compbio.ws.server.MafftWS +
      +
    getLimits() - +Method in class compbio.ws.server.MuscleWS +
      +
    getLimits() - +Method in class compbio.ws.server.ProbconsWS +
      +
    getLimits() - +Method in class compbio.ws.server.TcoffeeWS +
      +
    GetLimitsResponse - Class in compbio.data.msa.jaxws
     
    GetLimitsResponse() - +Constructor for class compbio.data.msa.jaxws.GetLimitsResponse +
      +
    getLocalPath() - +Static method in class compbio.engine.conf.PropertyHelperManager +
    Method return the absolute path to the project root directory. +
    getMax() - +Method in class compbio.metadata.ValueConstrain +
      +
    getMaxVMem() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getMclRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getMemoryLimit() - +Method in enum compbio.engine.cluster.dundee._Queue +
    return max memory limit in Mb +
    getMemoryStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.JobExecutionExceptionBean +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.JobSubmissionExceptionBean +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.ResultNotAvailableExceptionBean +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean +
      +
    getMessage() - +Method in class compbio.data.msa.jaxws.WrongParameterExceptionBean +
      +
    getMetadata() - +Method in class compbio.data.sequence.Alignment +
      +
    getMin() - +Method in class compbio.metadata.ValueConstrain +
      +
    getName() - +Method in interface compbio.metadata.Argument +
      +
    getName() - +Method in class compbio.metadata.Option +
    Human readable name of the option +
    getName() - +Method in class compbio.metadata.Preset +
      +
    getName() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getNativeSpec() - +Method in class compbio.runner._NativeSpecHelper +
      +
    getNativeSpecs() - +Method in interface compbio.engine.client.ClusterNativeSpecExecutable +
      +
    getNativeSpecs() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getNetNglycRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getNextPosition() - +Method in class compbio.metadata.ChunkHolder +
      +
    getNumberOfSequencesAllowed() - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    getNumberOfSequencesAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getOBRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getOnelineFasta() - +Method in class compbio.data.sequence.FastaSequence +
      +
    getOptionName() - +Method in class compbio.metadata.Parameter +
      +
    getOptionNames() - +Method in class compbio.metadata.Option +
      +
    getOptions() - +Method in class compbio.data.msa.jaxws.CustomAlign +
      +
    getOptions() - +Method in class compbio.metadata.Preset +
      +
    getOptions() - +Method in class compbio.metadata.RunnerConfig +
      +
    getOptionsAtRandom() - +Method in class compbio.runner.OptionCombinator +
      +
    getOutput() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getOutput() - +Method in interface compbio.engine.client.Executable +
      +
    getOutput() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getOutput() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getOutput() - +Method in class compbio.runner._impl.NetNglyc +
      +
    getOutput() - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getParameters() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.engine.client.ConfExecutable +
      +
    getParameters() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getParameters(Executable.ExecProvider) - +Method in interface compbio.engine.client.Executable +
      +
    getParameters() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getParameters() - +Method in class compbio.metadata.RunnerConfig +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.runner._impl.NetNglyc +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getParameters(Executable.ExecProvider) - +Method in class compbio.runner.msa.Tcoffee +
      +
    getParamValue(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    getPosition() - +Method in class compbio.data.msa.jaxws.PullExecStatistics +
      +
    getPosition() - +Method in class compbio.data.msa.jaxws.PullFile +
      +
    getPossibleValues() - +Method in interface compbio.metadata.Argument +
      +
    getPossibleValues() - +Method in class compbio.metadata.Option +
    List of possible optionNames +
    getPossibleValues() - +Method in class compbio.metadata.Parameter +
    List is more convenient to work with +
    getPreset() - +Method in class compbio.data.msa.jaxws.PresetAlign +
      +
    getPreset() - +Method in class compbio.metadata.Limit +
      +
    getPresetByName(String) - +Method in class compbio.metadata.PresetManager +
      +
    getPresetName() - +Method in class compbio.data.msa.jaxws.GetLimit +
      +
    GetPresets - Class in compbio.data.msa.jaxws
     
    GetPresets() - +Constructor for class compbio.data.msa.jaxws.GetPresets +
      +
    getPresets() - +Method in interface compbio.data.msa.MsaWS +
    Get presets supported by a web service +
    getPresets() - +Method in class compbio.metadata.PresetManager +
      +
    getPresets(Class<? extends Executable<T>>) - +Static method in class compbio.runner.Util +
      +
    getPresets() - +Method in class compbio.ws.server.ClustalWS +
      +
    getPresets() - +Method in class compbio.ws.server.MafftWS +
      +
    getPresets() - +Method in class compbio.ws.server.MuscleWS +
      +
    getPresets() - +Method in class compbio.ws.server.ProbconsWS +
      +
    getPresets() - +Method in class compbio.ws.server.TcoffeeWS +
      +
    GetPresetsResponse - Class in compbio.data.msa.jaxws
     
    GetPresetsResponse() - +Constructor for class compbio.data.msa.jaxws.GetPresetsResponse +
      +
    getPrmSeparator() - +Method in class compbio.metadata.RunnerConfig +
      +
    getProgram() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    GetProgress - Class in compbio.data.msa.jaxws
     
    GetProgress() - +Constructor for class compbio.data.msa.jaxws.GetProgress +
      +
    getProgress() - +Method in class compbio.engine.FilePuller +
      +
    getProgress(String) - +Static method in class compbio.engine.ProgressGetter +
      +
    getProgress(String) - +Static method in class compbio.ws.server.WSUtil +
      +
    GetProgressResponse - Class in compbio.data.msa.jaxws
     
    GetProgressResponse() - +Constructor for class compbio.data.msa.jaxws.GetProgressResponse +
      +
    getPropertyHelper() - +Static method in class compbio.engine.conf.PropertyHelperManager +
    Ways to fix path problem: 1) find a path to WEB-INF directory based on + the path to a known class. +
    getPSIBlastRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getQueue(int, int) - +Static method in enum compbio.engine.cluster.dundee._Queue +
      +
    getQueue(String) - +Method in enum compbio.engine.cluster.dundee._Queue +
      +
    getQueue() - +Method in class compbio.runner._NativeSpecHelper +
      +
    getQueueByMemoryRequirements(int) - +Static method in enum compbio.engine.cluster.dundee._Queue +
      +
    getRawUsage() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getRecordedJobStatus(String) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    getRemoteAddress(WebServiceContext) - +Static method in class compbio.ws.server.WSUtil +
      +
    GetResult - Class in compbio.data.msa.jaxws
     
    GetResult() - +Constructor for class compbio.data.msa.jaxws.GetResult +
      +
    getResult(String) - +Method in interface compbio.data.msa.MsaWS +
    Return the result of the job. +
    getResult(String) - +Method in class compbio.ws.server.ClustalWS +
      +
    getResult(String) - +Method in class compbio.ws.server.MafftWS +
      +
    getResult(String) - +Method in class compbio.ws.server.MuscleWS +
      +
    getResult(String) - +Method in class compbio.ws.server.ProbconsWS +
      +
    getResult(String) - +Method in class compbio.ws.server.TcoffeeWS +
      +
    GetResultResponse - Class in compbio.data.msa.jaxws
     
    GetResultResponse() - +Constructor for class compbio.data.msa.jaxws.GetResultResponse +
      +
    getResults(String) - +Method in interface compbio.engine.AsyncExecutor +
    Retrieve the results of the job. +
    getResults() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getResults(String) - +Method in class compbio.engine.client.ConfExecutable +
      +
    getResults() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getResults(String) - +Method in interface compbio.engine.client.Executable +
      +
    getResults(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    getResults(String) - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getResults(String) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    getResults(Future<ConfiguredExecutable<?>>, String) - +Static method in class compbio.engine.local.LocalEngineUtil +
      +
    getResults(String) - +Method in class compbio.runner._impl.NetNglyc +
      +
    getResults(String) - +Method in class compbio.runner._SkeletalCommandBuilder +
      +
    getResults(String) - +Method in class compbio.runner.msa.ClustalW +
      +
    getResults(String) - +Method in class compbio.runner.msa.Mafft +
      +
    getResults(String) - +Method in class compbio.runner.msa.Muscle +
      +
    getResults(String) - +Method in class compbio.runner.msa.Probcons +
      +
    getResults(String) - +Method in class compbio.runner.msa.Tcoffee +
      +
    getResults(String) - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.AlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.CustomAlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetJobStatusResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetLimitResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetLimitsResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetPresetsResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetProgressResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetResultResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.GetRunnerOptionsResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.PresetAlignResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.PullExecStatisticsResponse +
      +
    getReturn() - +Method in class compbio.data.msa.jaxws.PullFileResponse +
      +
    getRonnRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getRPSBlastDatabasesDir() - +Static method in class compbio.runner._impl.Environment +
      +
    getRPSBlastRunnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getRunConfiguration() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getRunnerClassName() - +Method in class compbio.engine.client.RunConfiguration +
      +
    getRunnerClassName() - +Method in class compbio.metadata.PresetManager +
      +
    getRunnerClassName() - +Method in class compbio.metadata.RunnerConfig +
      +
    getRunnerLimits(Class<? extends Executable<V>>) - +Static method in class compbio.engine.client.ConfExecutable +
    This method should be executed once and result of its execution reused. +
    GetRunnerOptions - Class in compbio.data.msa.jaxws
     
    GetRunnerOptions() - +Constructor for class compbio.data.msa.jaxws.GetRunnerOptions +
      +
    getRunnerOptions() - +Method in interface compbio.data.msa.MsaWS +
    Get options supported by a web service +
    getRunnerOptions(Class<? extends Executable<V>>) - +Static method in class compbio.engine.client.ConfExecutable +
      +
    getRunnerOptions() - +Method in class compbio.ws.server.ClustalWS +
      +
    getRunnerOptions() - +Method in class compbio.ws.server.MafftWS +
      +
    getRunnerOptions() - +Method in class compbio.ws.server.MuscleWS +
      +
    getRunnerOptions() - +Method in class compbio.ws.server.ProbconsWS +
      +
    getRunnerOptions() - +Method in class compbio.ws.server.TcoffeeWS +
      +
    GetRunnerOptionsResponse - Class in compbio.data.msa.jaxws
     
    GetRunnerOptionsResponse() - +Constructor for class compbio.data.msa.jaxws.GetRunnerOptionsResponse +
      +
    getRunnerPresets(Class<? extends Executable<V>>) - +Static method in class compbio.engine.client.ConfExecutable +
      +
    getSchema(String) - +Static method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    getSeqNumber() - +Method in class compbio.metadata.Limit +
      +
    getSequence() - +Method in class compbio.data.sequence.FastaSequence +
    Gets the value of sequence +
    getSequenceLenghtActual() - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    getSequenceLenghtActual() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequenceLenghtAllowed() - +Method in class compbio.data.msa.jaxws.LimitExceededExceptionBean +
      +
    getSequenceLenghtAllowed() - +Method in exception compbio.metadata.LimitExceededException +
      +
    getSequences() - +Method in class compbio.data.sequence.Alignment +
      +
    getServiceName(String[]) - +Static method in class compbio.ws.client.Jws2Client +
    Extracts service name from the command line +
    getSession() - +Method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getSize() - +Method in class compbio.data.sequence.Alignment +
      +
    getStartTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getStatFile() - +Static method in class compbio.runner.msa.ClustalW +
      +
    getStatFile() - +Static method in class compbio.runner.msa.Muscle +
      +
    getStatistics(JobInfo) - +Static method in class compbio.engine.cluster.drmaa.ClusterSession +
      +
    getSubmissionTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getSupportedOptions(Class<? extends Executable<T>>) - +Static method in class compbio.runner.Util +
      +
    getSupportedRuntimes() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getSupportedRuntimes() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getSupportedRuntimes(Class<?>) - +Static method in class compbio.engine.client.Util +
      +
    getSyncEngine(ConfiguredExecutable<?>, Executable.ExecProvider) - +Static method in class compbio.engine.Configurator +
      +
    getSyncEngine(ConfiguredExecutable<?>) - +Static method in class compbio.engine.Configurator +
      +
    getTask(String) - +Static method in class compbio.engine.SubmissionManager +
      +
    getTaskDirectory(Class<?>) - +Static method in class compbio.engine.conf.DirectoryManager +
      +
    getTaskId() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getTaskId() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getTaskId() - +Method in class compbio.engine.Job +
      +
    getTestArgs() - +Static method in class compbio.runner._impl.Disembl +
      +
    getTestArgs() - +Static method in class compbio.runner._impl.NetNglyc +
      +
    getTestArgs() - +Method in class compbio.runner._impl.OB +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.Disembl +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.Mcl +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.NetNglyc +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.OB +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.Ronn +
      +
    getTestCommand() - +Static method in class compbio.runner._impl.RPSBlast +
      +
    getTestParams() - +Static method in class compbio.runner._impl.Mcl +
      +
    getTimeLimit() - +Method in enum compbio.engine.cluster.dundee._Queue +
    0 - unlimited +
    getTimeStat() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getTmhmm2Runnable(String) - +Static method in class compbio.runner._impl.Runners +
      +
    getType() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    getType() - +Method in class compbio.metadata.ValueConstrain +
      +
    getType() - +Method in class compbio.runner.msa.ClustalW +
      +
    getType() - +Method in class compbio.runner.msa.Mafft +
      +
    getType() - +Method in class compbio.runner.msa.Muscle +
      +
    getType() - +Method in class compbio.runner.msa.Probcons +
      +
    getType() - +Method in class compbio.runner.msa.Tcoffee +
      +
    getType() - +Method in class compbio.runner.psiblast.PsiBlast +
      +
    getUsedSysTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getUsedUserTime() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getValidator(String) - +Static method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    getValidator(Schema) - +Static method in class compbio.engine.conf.RunnerConfigMarshaller +
      +
    getValidValue() - +Method in class compbio.metadata.Parameter +
      +
    getVMem() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    getWorkDirectory(String) - +Method in interface compbio.engine.AsyncExecutor +
      +
    getWorkDirectory() - +Method in class compbio.engine.client.ConfExecutable +
      +
    getWorkDirectory() - +Method in interface compbio.engine.client.ConfiguredExecutable +
      +
    getWorkDirectory(String) - +Method in class compbio.engine.cluster.drmaa.AsyncJobRunner +
      +
    getWorkDirectory() - +Method in class compbio.engine.cluster.drmaa.JobRunner +
      +
    getWorkDirectory(String) - +Static method in class compbio.engine.Configurator +
      +
    getWorkDirectory(String) - +Method in class compbio.engine.local.AsyncLocalRunner +
      +
    getWorkDirectory() - +Method in class compbio.engine.local.LocalRunner +
      +
    getWorkDirectory() - +Method in interface compbio.engine.SyncExecutor +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
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    +    		 + +
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    +
    +
    hasDump() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    hasExited() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    hashCode() - +Method in class compbio.data.sequence.AlignmentMetadata +
      +
    hashCode() - +Method in class compbio.engine.client.CommandBuilder +
      +
    hashCode() - +Method in class compbio.engine.client.RunConfiguration +
      +
    hashCode() - +Method in class compbio.engine.client.SkeletalExecutable +
      +
    hashCode() - +Method in class compbio.engine.ClusterJobId +
      +
    hashCode() - +Method in class compbio.engine.conf._Key +
      +
    hashCode() - +Method in class compbio.engine.FilePuller +
      +
    hashCode() - +Method in class compbio.engine.Job +
      +
    hashCode() - +Method in class compbio.metadata.ChunkHolder +
      +
    hashCode() - +Method in class compbio.metadata.Limit +
      +
    hashCode() - +Method in class compbio.metadata.Option +
      +
    hashCode() - +Method in class compbio.metadata.Parameter +
      +
    hashCode() - +Method in class compbio.metadata.Preset +
      +
    hashCode() - +Method in class compbio.metadata.ValueConstrain +
      +
    hashCode() - +Method in class compbio.pipeline._jpred.PScore +
      +
    hasMoreData() - +Method in class compbio.engine.FilePuller +
      +
    hasParam(String) - +Method in class compbio.engine.client.CommandBuilder +
      +
    hasSignaled() - +Method in class compbio.engine.cluster.drmaa.StatisticManager +
      +
    hasTimeLimit() - +Method in enum compbio.engine.cluster.dundee._Queue +
      +
    +
    + + + + + + + + + + + + + + + +
    + + + + + + + + + + + + +
    Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
    +    		 + +
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    +
    +
    initPull() - +Method in class compbio.engine.FilePuller +
      +
    IS_CLUSTER_ENGINE_ENABLED - +Static variable in class compbio.engine.Configurator +
      +
    IS_LOCAL_ENGINE_ENABLED - +Static variable in class compbio.engine.Configurator +
      +
    isAbsolutePath(String) - +Static method in class compbio.engine.client.PathValidator +
    Whether a certain path is absolute or not is operation system dependent! +
    isAmbiguosProtein(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Check whether the sequence confirms to amboguous protein sequence +
    isDefault() - +Method in class compbio.metadata.Limit +
      +
    isExceeded(List<FastaSequence>) - +Method in class compbio.metadata.Limit +
    Checks if the number of sequences or their average length in the dataset + exceeds limits the values defined by this Limit +
    isFileCreated() - +Method in class compbio.engine.FilePuller +
      +
    isMarked(String, JobStatus) - +Static method in class compbio.engine.client.Util +
      +
    isNonAmbNucleotideSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
    Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one + (!) - B char +
    isNucleotideSequence(FastaSequence) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isProteinSequence(String) - +Static method in class compbio.data.sequence.SequenceUtil +
      +
    isRequired() - +Method in class compbio.metadata.Option +
    Flag that indicated that this option must be specified in the command + line for an executable to run +
    isReturn() - +Method in class compbio.data.msa.jaxws.CancelJobResponse +
      +
    isShutdown() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    isTerminated() - +Method in class compbio.engine.local._TrackingExecutor +
      +
    isValidClustalFile(InputStream) - +Static method in class compbio.data.sequence.ClustalAlignmentUtil +
      +
    isValidDirectory(String) - +Static method in class compbio.engine.client.PathValidator +
      +
    isValidExecutable(String) - +Static method in class compbio.engine.client.PathValidator +
      +
    isValidJobId(String) - +Static method in class compbio.engine.client.Util +
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    compbio.data._structure 
    compbio.data.msa 
    compbio.data.msa.jaxws 
    compbio.data.sequenceA data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    compbio.engine 
    compbio.engine.clientClasses and interfaces representing an input for engines.
    compbio.engine.cluster.drmaaAn cluster engine classes responsible for execution of Executables on the clusters.
    compbio.engine.cluster.dundee 
    compbio.engine.confClasses commonly used by both engines.
    compbio.engine.localAn local engine classes responsible for execution of Executables on the local computer + (the same machine as JVM running these classes).
    compbio.metadataA meta-data model for multiple sequence alignment web services + Classes in this package have no dependencies to other sources in the project.
    compbio.pipeline._jpred 
    compbio.runnerUtilities commonly used by all runners.
    compbio.runner._impl 
    compbio.runner._jpred 
    compbio.runner.msaWrappers for native executables for multiple sequence alignment (msa)
    compbio.runner.psiblast 
    compbio.ws.client 
    compbio.ws.server 
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    Package Hierarchies:
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    +Package compbio.data.sequence
    + +

    + + + + + +
    +Class compbio.data.sequence.UnknownFileFormatException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 196629543695636854L + +

    + + + + + +
    +Serialized Fields
    + +

    +file

    +
    +java.io.File file
    +
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    +Package compbio.metadata
    + +

    + + + + + +
    +Class compbio.metadata.JobExecutionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5477751361755778769L + +

    + +

    + + + + + +
    +Class compbio.metadata.JobSubmissionException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: 607986894357895572L + +

    + +

    + + + + + +
    +Class compbio.metadata.LimitExceededException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: 15066952180013505L + +

    + + + + + +
    +Serialized Fields
    + +

    +numberOfSequencesAllowed

    +
    +int numberOfSequencesAllowed
    +
    +
    +
    +
    +
    +

    +actualNumberofSequences

    +
    +int actualNumberofSequences
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtAllowed

    +
    +int aSequenceLenghtAllowed
    +
    +
    +
    +
    +
    +

    +aSequenceLenghtActual

    +
    +int aSequenceLenghtActual
    +
    +
    +
    +
    + +

    + + + + + +
    +Class compbio.metadata.ResultNotAvailableException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -5475613614578761L + +

    + +

    + + + + + +
    +Class compbio.metadata.UnsupportedRuntimeException extends JobSubmissionException implements Serializable
    + +

    +serialVersionUID: -86624836785110293L + +

    + +

    + + + + + +
    +Class compbio.metadata.WrongParameterException extends java.lang.Exception implements Serializable
    + +

    +serialVersionUID: -547775417557345769L + +

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zc9$@G`W8`QZh2blavllZvf}CF)~mirTk~~Jx&=EDG5d}WFMJOLnuUuR?9Cl%4jeUi%%q{pf@on93~WAy?dzIpfP9+nwv;-(4fgqv-@B=jj@!hSW0$!22G;L>30X6ZhxKC?Q(OoTCG8^ zH8|w$oWAP4diAmC=}%5KU;Xm`o_2h4ddM3L23>x9xx4|F-TTSu&S_luy{@}mUcVFn z2b^A))8leE{H{-4ogV7^B!0NF6Wa|nAFQsfKG-}hTJ?12!Oo%T=IQEAY&CVwg9=D)dwdg4j#COpQFc`F)3&s!Zo_OYXZG?vlca` z+EjL1wJ8H21oKQ1puHJl_&T4wJS)-ZWML#iwJ3F(|Q2q>c zW}&%Q-PwHoQM1)#GFj~=`s~qG@3enwZJpcSYjt0>YV9$5;xW+N{mCTF*2ktD*j4*u zk3DwvlaD>-^?CzW?X=(1cF+X9eml`j`!IxB9Pc z-FkJabt^UN*2lco$54jvcJ0?_u7c(oXuK*7;;Hj0t|e)_cIUKr8W>(WlXH^B>-TsN zLLR0WI!H8X)V%5#k{nJtQMyN?!Ol`$CYtF^%Wg`jT|?KdUE4j>d9As#neP5yU;X1h z!2Ut1vl#^$yJR661f@pv2L}-uyPrRZ-3>@lMS1>9U;64-zba@tRhs5qf!)r4E?z_j zwX3>%*Qwot2DJ&>f7P*D8p2C+jS~tnbPZwjb9zUC6Dna!*t~c9-8TPLm)C0bS`$f{ zrU22{yB4X+D4Uav~yZ*n;`8oNs40gd0~QfWL6&|C}9a$Azc z<767A#p$tl0&NZtXe5VPYaD?n?(le=QUC^)0G*RR$}|=awKk8_>4--IWJ*g8#qo75 zuv>D_0z~-baaz(L5U>QK(ZI@hU^mqoqKU>O>F1{`D`UGo_)%IC3_p5JLc4YiQ8 + + + +Java Bioinformatics Analyses Web Services (JABAWS) main +page + + + + +
    + + + +
    + + + +
    +

    +JAva Bioinformatics Analysis Web Services (JABAWS) is a collection of SOAP web services for Bioinformatics.
    +Currently JABAWS provides five web +services for multiple sequence alignment Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Unlike other web services you can run JABAWS services from your own computer. This puts you in control of the web services - they will be where and when you need them, have no restrictions and your data privacy is guaranteed. JABAWS scales well from the single user single computer to the cluster with hundreds of users. Finally, you do not have to be an expert to use JABAWS - the installation is simple and you can use the services from the comfort of your desktop via Jalview.

    +

    Public JABAWS Server

    +

    You can access our public JABA Web Services with our command line client, the Jalview, or write your own program. To guarantee a level service for everyone our public services impose some restrictions on the size and the number of the jobs you can submit. Currently we do not process tasks that exceed 1000 sequences per 1000 letters on average. Should you find this to be insufficient for your needs you can download and run JABAWS Server on your own hardware. This also applies if the privacy is a concern or an Internet connection is a problem.

    +
      +
    • The JABAWS public web services address is http://www.combio.dundee.ac.uk/jabaws
      • +
    • Detailed web services description is available from here: WSDL List
      • +
    +

    Contact Us

    +

    Please feel free to post your questions/issues to the jabaws-discuss mailing list.

    +

    Authors

    +

    Peter Troshin and Geoff Barton are the authors of the JABA Web +Services. Jim Procter helped with the JABAWS design process and web +pages, and developed the interface and management components in +Jalview to access JABAWS servers.

    +
    + + + +
    + + +
    + + + + + + + diff --git a/website/man_about.html b/website/man_about.html new file mode 100644 index 0000000..7196fc5 --- /dev/null +++ b/website/man_about.html @@ -0,0 +1,96 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) manual - About + + + + + + +
    + +
    + + +
    + +

    JABAWS MANUAL

    +

    About

    + + + + +

    What is JABAWS?

    +

    JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for multiple sequence alignment. For simplicity we referrer to them as JABAWS. Right now, JABAWS makes it easy to access well-known multiple sequence alignment programs from JalView. However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools. For the list of currently supported programs see here. JABAWS consists of the two parts - the server and the client. Unlike other web services you can download and use both on your own computer! If you want a server just for yourself, then download and install JABAWS Virtual Appliance. It requires no configuration and simple to install. If you want to install JABAWS for your own lab then download JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or interested in writing your own client, the JABAWS command line client is what you need.

    +

    JABAWS Benefits

    +

    JABAWS can be deployed on many operating system and operate as a stand alone server or submit the jobs to the cluster. Thanks to DRMAA it integrates well with a large variety of cluster job management systems. Jalview from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder.

    +

    JABA Web Services Programs

    +

    JABAWS currently uses the following programs under the hood

    +     + +

    What is JABAWS Server?

    +

    JABAWS Server is a Web Application which exposes a number of widely used Bioinformatics programs as SOAP web services. Currently it supports 5 multiple sequence alignment programs. You can download and install JABAWS on your own computer. JABAWS can be configured to execute programs on computer it is installed or submit them to the cluster. JABAWS provides the uniform API for each web service if supports.

    +

    What is JABAWS client?

    +

    JABAWS client is a command line Java application which can call all JABAWS methods on any instance of JABAWS Server, no matter local or remote. It is useful if you want to script against a JABAWS server and do not want to handle any web service specific details. We also offer a source code of the client so that you can find out how to work with JABA Web Services if you would like to write your own client software. JABAWS command line client offers the same functionality as Jalview when connected to JABAWS.

    +

    Programmatic access to JABAWS

    +

    JABA Web Services are WS-I basic profile compliant, they can be accessed in a standard way as any other web service. The WSDL for each service is published on the JABAWS home page. If you use Java, then you can use our client package to access JABAWS. This package contains value objects which you could alternatively generate with wsimport in Java, or similar tool in other language. On top of that it offers some additional methods which further simplify working with JABAWS. For more information please refer to the data model javadoc.

    +
    + +
    + + +
    + + + + + + + + diff --git a/website/man_client.html b/website/man_client.html new file mode 100644 index 0000000..dc651ab --- /dev/null +++ b/website/man_client.html @@ -0,0 +1,110 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Command Line Client manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    JABAWS Command Line Client Usage

    +

    The command line client comes as a part of client package which you are welcome to download. The command line client can be used to align sequences using any of JABAWS supported web services. The client is OS independent and supports most of the functions which can be accessed programmatically via JABAWS API. Using this client you could align sequences using presets or custom parameters, please see examples of this below. Here is the list of options supported by the command line client.

    +Usage: java -jar <path_to_jar_file> -h=host_and_context -s=serviceName ACTION [OPTIONS] +-h=<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.10.159:8080/ws
    +-s=<ServiceName> - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS] +

    +
    +ACTIONS:
    +-i=<inputFile> - full path to fasta formatted sequence file, from which to align sequences
    +-parameters - lists parameters supported by web service
    +-presets - lists presets supported by web service
    +-limits - lists web services limits
    +Please note that if input file is specified other actions are ignored +

    +
    + OPTIONS: (only for use with -i action):
    +-r=<presetName> - name of the preset to use
    +-o=<outputFile> - full path to the file where to write an alignment
    +-f=<parameterInputFile> - the name of the file with the list of parameters to use.
    +Please note that -r and -f options cannot be used together. Alignment is done with either preset or a parameters from the file, but not both!     +

    Align sequences from input.fasta file using Mafft web service with default settings, print alignment in Clustal format to console.

    +

    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta

    +

    Content of input.fasta file is show below (please note sequences has been trimmed for clarity)>Foobar
    + MTADGPRELLQLRAAVRHRPQDFVAWL
    + >Bar
    + MGDTTAGEMAVQRGLALHQ
    + QRHAEAAVLLQQASDAAPE
    + >Foofriend
    + MTADGPRELLQLRAAV

    +

    Align as in above example, but write output alignment in a file out.clustal, using parameters defined in prm.in file

    +

    java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -i=d:\input.fasta -o=d:\out.clustal -f=prm.in

    +

    The content of the prm.in file is shown below --nofft
    + --noscore
    + --fastaparttree
    + --retree=10
    + --op=2.2

    +

    The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but the setting controlling output are not. This is due to the fact the output have to be handled by JABAWS, so must remain within its control. For a list of parameters supported by a web service see the next example. In prm.in parameters are separated by the new line, and name of the parameter is separated from its value with an equal sign. This format is constant no matter which JABAWS web service is used.
    + java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters

    +

    The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used -h=http://myhost.compbio.ac.uk:8080/jabaws server, now you want to use another server to -h=http://mylabserver.myuni.edu. This comes handy if your favorite server is off and you need to do the job yesterday.

    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/man_configuration.html b/website/man_configuration.html new file mode 100644 index 0000000..8c18617 --- /dev/null +++ b/website/man_configuration.html @@ -0,0 +1,436 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Server Configuration manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    JABAWS Configuration

    + +

    JABAWS Configuration

    +

    There are three parts of the system you can configure. The local +and the cluster engines, and the paths to the individual executables for +each engine. These settings are stored in configuration files +within the web application directory (for an overview, then take a +look at the war file content table).

    +

    Initially, JABAWS is configured with only the local engine + enabled, with job output written to directory called "jobsout" + within the web application itself. This means that JABAWS will work + out of the box, but may not be suitable for serving a whole lab or + a university.

    +

    Local Engine Configuration

    + +

    The Local execution engine configuration is defined in the +properties file conf/Engine.local.properties. The supported +configuration settings are:
    + engine.local.enable=true - # +enable or disable local engine, valid values true | false
    + local.tmp.directory=D:\\clusterengine\\testoutput +- a directory to use for temporary files storage, optional, +defaults to java temporary directory
    + engine.local.thread.number=4 - +Number of threads for tasks execution (valid values between 1 and +2x cpu. Where x is a number of cores available in the system). +Optional defaults to the number of cores for core number <=4 and +number of cores-1 for greater core numbers.

    + +

    If the local engine going to be heavily loaded (which is often the case if you do not have a cluster) it is a good idea to increase +the amount of memory available for the web application server. If +you are using Apache-Tomcat, then you can define its memory +settings in the JAVA_OPTS environment variable. To specify which +JVM to use for Apache-Tomcat, put the full path to the JRE +installation in the JAVA_HOME environment variable (We would +recommend using Sun Java Virtual Machine (JVM) in preference to +Open JDK). Below is an example of code which can be added to <tomcat_dir>/bin/setenv.sh script +to define which JVM to use and a memory settings for Tomcat server. +Tomcat server startup script (catalina.sh) will execute setenv.sh on each server start +automatically.
    + export +JAVA_HOME=/homes/ws-dev2/jdk1.6.0_17/
    + export JAVA_OPTS="-server -Xincgc -Xms512m -Xmx1024m"

    + +

    Cluster Engine Configuration

    + +

    Supported configuration settings:
    + engine.cluster.enable=true - # +enable or disable local engine true | false, defaults to +false
    + cluster.tmp.directory=/homes/clustengine/testoutput- +a directory to use for temporary files storage. The value must be +an absolute path to the temporary directory. Required. The value +must be different from what is defined for local engine. This +directory must be accessible from all cluster nodes.
    + For the cluster engine to work, the SGE_ROOT and LD_LIBRARY_PATH +environment variables have to be defined. They tell the cluster +engine where to find DRMAA libraries. These variables +should be defined when the web application server starts up, e.g.

    + +

    SGE_ROOT=/gridware/sge
    + LD_LIBRARY_PATH=/gridware/sge/lib/lx24-amd64

    + +

    Finally, do not forget to configure executables for the cluster +execution, they may be the same as for the local execution but may +be different. Please refer to the executable configuration section +for further details.

    + +

    Executable Configuration

    + +

    All the executable programs +are configured in conf/Executable.properties file. Each executable +is configured with a number of options. They are: local.X.bin.windows=<path to executable under windows +system, optional>
    + local.X.bin=<path to the executable under non-windows system, +optional>
    + cluster.X.bin=<path to the executable on the cluster, all +cluster nodes must see it, optional>
    + X.bin.env=<semicolon separated list of environment variables +for executable, use hash symbol as name value separator, +optional>
    + X.--aamatrix.path=<path to the directory containing +substitution matrices, optional>
    + X.presets.file=<path to the preset configuration file, optional +>
    + X.parameters.file=<path to the parameters configuration file, +optional>
    + X.limits.file=<path to the limits configuration file, +optional>
    + X.cluster.settings=<list of the cluster specific options, +optional>

    + +

    Where X is either clustal, muscle, mafft, probcons or tcoffee.

    + +

    Default JABAWS configuration includes path to local executables +to be run by the local engine only, all cluster related settings +are commented out, but they are there for you as example. Cluster +engine is disabled by default. To configure executable for cluster +execution un comment the X.cluster settings and change them +appropriately.

    +

    By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.
    + After you have completed the editing your configuration may look like + this:local.mafft.bin.windows=
    + local.mafft.bin=binaries/mafft
    + cluster.mafft.bin=/homes/cengine/mafft
    + mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;
    + mafft.--aamatrix.path=binaries/matrices
    + mafft.presets.file=conf/settings/MafftPresets.xml
    + mafft.parameters.file=conf/settings/MafftParameters.xml
    + mafft.limits.file=conf/settings/MafftLimits.xml
    + mafft.cluster.settings=-q bigmem.q -l h_cpu=24:00:00 -l + h_vmem=6000M -l ram=6000M

    +

    Please not that relative paths must only be specified for the +files that reside inside web application directory, all other paths +must be supplied as absolute!

    + +

    Furthermore, you should avoid using environment variables within the paths or options - since these will not be evaluated correctly. Instead, please explicitly +specify the absolute path to anything +normally evaluated from an environment variable at execution time.

    + +

    If you are using JABAWS to submit jobs to the cluster (with +cluster engine enabled), executables must be available from all +cluster nodes the task can be sent to, also paths to the +executables on the cluster e.g. cluster.<exec_name>.bin must be +absolute.

    + +

    Executables can be located anywhere in your system, they do not +have to reside on the server as long as the web application server +can access and execute them.

    + +

    Cluster settings are treated as a black box, the system will +just pass whatever is specified in this line directly to the +cluster submission library. This is how DRMAA itself treats this +settings. More exactly DRMAA JobTemplate.setNativeSpecification() function will be called.

    + +

    Defining Environment Variables for +Executables

    + +

    Environment variables can be defined in property x.bin.env Where x is +one of five executables supported by JABAWS. Several environment +variables can be specified in the same line. For example.
    + mafft.bin.env=MAFFT_BINARIES#/homes/cengine/mafft;FASTA_4_MAFFT#/bin/fasta34;

    + +

    The example above defines two environment variables with names +MAFFT-BINARIES and FASTA_4_MAFFT and values /homes/cengine/mafft +and /bin/fasta34 respectively. Semicolon is used as a separator +between different environment variables whereas hash is used as a +separator for name and value of the variable.

    + +

    Configure JABAWS to Work +with Mafft

    + +

    If you use default configuration you do not need to read any +further. The default configuration will work for you without any +changes, however, if you want to install Mafft yourself then there +is a couple of more steps to do.

    + +

    Mafft executable needs to know the location of other files +supplied with Mafft. In addition some Mafft functions depends on +the fasta executable, which is not supplied with Mafft, but is a +separate package. Mafft needs to know the location of fasta34 +executable.

    + +

    To let Mafft know where the other files from its package are +change the value of MAFFT-BINARIES environment variables. To let +Mafft know where is the fasta34 executable set the value of +FASTA_4_MAFFT environment variable to point to a location of +fasta34 program. The latter can be added to the PATH variable +instead. If you are using executables supplied with JABAWS, the +path to Mafft binaries would be like <relative path to web application +directory>/binaries/src/mafft/binaries and the path to +fasta34 binary would be <relative path +to web application +directory>/binaries/src/fasta34/fasta34. You can specify +the location of Mafft binaries as well as fasta34 program elsewhere +by providing an absolute path to them. All these settings are +defined in conf/Executable.properties file.

    +

    Limiting the size of the job accepted by JABAWS

    +

    JABAWS can be configured to reject excessively large tasks. This is useful if you operate JABAWS service for many users. By defining a maximum allowed task size you can provide an even service for all users and prevents waist of resources on the tasks too large to complete successfully. You can define the maximum number of sequences and the maximum average sequence length that JABAWS accepts for each JABA Web Service independently. +Furthermore, you can define different limits for different presets of the same web service.
    +By default limits are set well in excess of what you may want to offer to the users outside your lab, to make sure that the tasks are never rejected. The default limit is 100000 sequences of 100000 letters on average for all of the JABA web services. You can adjust the limits according to your needs by editing conf/settings/<X>Limit.xml files.

    +

    Using a different version of the alignment program with JABAWS

    +

    JABAWS supplied with binaries and source code of the executables which version it supports. So normally you would not need to install your own executables. However, if you have a different version of an executable (e.g. an alignment program) which you prefer, you could use it as long as it supports all the functions JABAWS executable supported. This could be the case with more recent executable. If the options supported by your chosen executable is different when the standard JABAWS executable, than you need to edit ExecutableNameParamaters.xml  configuration file.

    +

    Load balancing

    +

    If your cluster is busy and have significant waiting times you can achieve a faster response by allowing the server machine to calculate small tasks and the reserve the cluster for bigger jobs. This works especially well if your server is a powerful machine with many CPUs. To do this you need to enable and configure both the cluster and the local engines. Once this is done decide on the maximum size of a task to be run on the server locally. Then, edit "# LocalEngineExecutionLimit #" preset in <ServiceName>Limits.xml file accordingly. JABAWS server then will balance the load according to the following rule: If the task size is smaller then the maximum task size for local engine, and the local engine has idle threads, then calculate task locally otherwise submit the task to the cluster.

    +

    Reviewing JABAWS configuration via web browser

    +

    Access to configuration files is prohibited to any unauthorized users by means of security constrain defined in web application descriptor file. There is a special user role called admin who can access these files. This comes handy if you would like to keep an eye on any of the task outputs stored in jobsout, or would like to view the configuration files. To access the configuration files add admin user into your application server. The way you do it depends on where you would like the user passwords to come from and your web application server. If you use Tomcat, then the simplest way is to use Tomcat Memory Realm which is linked to a plain text configuration file. To define the user in Tomcat server add an entry in conf/tomcat-user.xml file. <role rolename="admin"/>
    + <user username="admin" password="your password here " roles="admin"/>

    +

    Once this is done make sure the servlet that returns the web application directory listings is enabled. Look in the <tomcatroot>/conf/web.xml file for the following <param-name>listings</param-name>
    + <param-value>true</param-value>

    +

    The whole section that defines default listing servlet is below

    +

    <servlet>
    + <servlet-name>default</servlet-name>
    + <servlet-class>org.apache.catalina.servlets.DefaultServlet</servlet-class>
    + <init-param>
    + <param-name>debug</param-name>
    + <param-value>0</param-value>
    + </init-param>
    + <init-param>
    + <param-name>listings</param-name>
    + <param-value>true</param-value>
    + </init-param>
    + <load-on-startup>1</load-on-startup>
    + </servlet>
    +

    +

    These listings are read only by default.

    +

    Testing JABA Web Services

    +

    You can use a command line client (part of the client only + package) to test your JABAWS installation as described here. If you downloaded a JABAWS + server package, you can use <your_jaba_context_name>/WEB-INF/lib/jaba-client.jar to test JABAWS installation as described in here. If you downloaded the source + code, then you could run a number of test suits defined in the + build.xml Apache Ant file.

    +

    JABAWS requests logging

    +

    Enable Tomcat log valve. To do this uncomment the following section of <tomcat_root>/conf/server.xml configuration file.

    +

    <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs"
    + prefix="localhost_access_log." suffix=".txt" pattern="common" resolveHosts="false"/>

    +

    The following information will be logged:

    + + + + + + + + + + + + + + + +
    Remote IPDateMethod server_URL protocol HTTP status Response size in bytes
    10.31.11.159[10/Feb/2010:16:51:32 +0000]"POST /jws2/MafftWS HTTP/1.1"2002067
    +

    Which can be processed in various programs for log analysis , such as WebAlizer, Analog, AWStats.

    +

    JABAWS internal logging

    +

    JABAWS can be configured to log what it is doing. This comes + handy if you would like to see who is using your web services or + need to chase some problems. JABAWS uses log4j to do the logging, + the example of log4j configuration is bundled with JABAWS war file. + You will find it in the /WEB-INF/classes/log4j.properties file. All the + lines in this file are commented out. The reason why the logging is + disabled by default it simple, log4j have to know the exact + location where the log files should be stored. This is not known up + until the deployment time. To enable the logging you need to + define logDir property in the log4j.properties and uncomment section of + the file which corresponds to your need. More information is given + in the log4j.properties file + itself. Restart the Tomcat or the JABAWS web application to apply + the settings.

    +

    After you have done this, assuming that you did not change the + log4j.properties file yourself, you should see the application log + file called activity.log. The + amount of information logged can be adjusted using different + logging levels, it is reduced in the following order of log levels + TRACE, DEBUG, INFO, WARN, ERROR, FATAL.

    +

    If you would like to know who is using your services, you might + want to enable Tomcat request + logging.

    +

    Monitoring JABAWS

    +

    JABAWS stores cluster task ids for all tasks which were run on the cluster. Using cluster ids the detailed statistics can be extracted from cluster accounting system. Due to the fact that each cluster supported by JABAWS have different accounting system it was not possible to provide ready to use statistics.
    + For the local execution the starting and finishing time in nano seconds can be found in STARTED and FINISHED files respectively. In time we will provide the tools to extract execution time statistics, so keep the content of your working directory ready!

    +

    JABAWS War File Content

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    DirectoryContent description
    conf/contains configuration files such as Executable.properties, + Engine.local.properties, Engine.cluster.properties
    conf/settingsContains individual executable description files. In particular + XXXParameters.xml, XXXPresets.xml, XXXLimits.xml where XXX is the + name of the executable
    jobsout/Contains directories generated when running an individual executable. E.g. input and output files and some other task + related data. (optional)
    binaries/Directory contains native executables - programs, + windows binaries (optional)
    binaries/srcContains source of native executables and Linux i386 + binaries.
    binaries/matricesSubstitution matrices +
    WEB-INFWeb application descriptor
    WEB-INF/libWeb application libraries
    WEB-INF/classeslog4j.properties - log configuration file (optional)
    Help Pages
    /help pages, index.html is the starting page
    dm_javadocjavadoc for JABAWS client (the link is available from How To + pages)
    prog_docsdocumentation for programs that JABAWS uses
    imagesimages referenced by html pages
    +

     

    +
    + + +
    + + +
    + + + + + + + + diff --git a/website/man_dev.html b/website/man_dev.html new file mode 100644 index 0000000..f16691d --- /dev/null +++ b/website/man_dev.html @@ -0,0 +1,358 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) client developers manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    Using JABAWS From Your Program

    + +

    Web services functions overview

    +

    All JABA multiple sequence alignment web services comply to the same interface, thus the function described below are available from all the services.

    +

    Functions for initiating the alignment String id = align(List<FastaSequence> list)
    + String id = customAlign(List<FastaSequence> sequenceList, List<Option> optionList)
    + String id = presetAlign(List<FastaSequence> sequenceList, Preset preset)

    +

    Functions pertaining to job monitoring and control
    + JobStatus status = getJobStatus(String id)
    + Alignment al = getResult(String id)
    + boolean cancelled = cancelJob(String id)
    + ChunkHolder chunk = pullExecStatistics(String id, long marker)

    +

    Functions relating to service features discovery
    + RunnerConfig rc = getRunnerOptions()
    + Limit limit = getLimit(String name)
    + LimitsManager lm = getLimits()
    + PresetManager pm = getPresets()

    +

    Please refer to a data model javadoc for a detailed description of each methods.

    +

    Structure of the template command line client

    + + + + + + + + + + + + + + + + + + + + + +
    PackagesClasses and Interfaces
    compbio.data.msa MsaWS the interface for all multiple sequence alignment web services
    compbio.data.sequenceJABAWS data types
    compbio.metadataJABAWS meta data types
    compbio.ws.clientJABAWS command line client
    +

    Additional utility libraries this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.
    + Please refer to a data model javadoc for a detailed description of each class and its methods.

    +

    Connecting to JABAWS

    +

    For a complete working example of JABAWS command line client please see compbio.ws.client.Jws2Client class. JABAWS command line client source code is available from the download page. Please note that for now all the examples are in Java other languages will follow given a sufficient demand.

    +

    Download a binary JABAWS client. Add the client to the class path. The following code excerpt will connect your program to Clustal web service deployed in the University of Dundee.

    +

    import java.net.URL;
    + import javax.xml.namespace.QName;
    + import javax.xml.ws.Service;
    + ...............
    + 1) String qualifiedName = "http://msa.data.compbio/01/01/2010/";
    + 2) URL url = new URL("http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");
    + 3) QName qname = new QName(, "ClustalWS");
    + 4) Service serv = Service.create(url, qname);
    + 5) MsaWS msaws = serv.getPort(new QName(qualifiedName, "ClustalWSPort"), + MsaWS.class);

    +

    Line 1 makes a qualified name for JABA web services.
    + Line 2 + constructs the URL to the web services WSDL.
    + Line 3 makes a qualified name instance for Clustal JABA web service.
    + Line 4 creates a service instance.
    + Line 5 makes a connection to the server.

    +

    A more generic connection method would look like this

    +

    import java.net.URL;
    + import javax.xml.namespace.QName;
    + import javax.xml.ws.Service;
    + import compbio.ws.client.Services
    + ..............
    + String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
    + String host = "http://www.compbio.dundee.ac.uk/jabaws";
    + // In real life the service name can come from args
    + Services clustal = Services.ClustalWS;
    + URL url = new URL(host + "/" + clustal.toString() + "?wsdl");
    + QName qname = new QName(qualifiedServiceName, clustal.toString());
    + Service serv = Service.create(url, qname);
    + MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, clustal
    + + "Port"), MsaWS.class);

    +

    Where Services is enumeration of JABAWS web services. All JABAWS multiple sequence alignment methods confirm to MsaWS specification, thus from the caller point of view all JABAWS web services can be represented by MsaWS interface. The full documentation of MsaWS functions is available from the javadoc.

    +

    Valid JABAWS service names and WSDL files

    +
      +
    • ClustalWS (http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl)
      • +
    • MuscleWS (http://www.compbio.dundee.ac.uk/jabaws/MuscleWS?wsdl)
      • +
    • MafftWS (http://www.compbio.dundee.ac.uk/jabaws/MafftWS?wsdl)
      • +
    • TcoffeeWS (http://www.compbio.dundee.ac.uk/jabaws/TcoffeeWS?wsdl)
      • +
    • ProbconsWS (http://www.compbio.dundee.ac.uk/jabaws/ProbconsWS?wsdl)
      • +
    +

    Aligning sequences

    +

    Given that msaws is web service proxy, created as described in "Connecting to JABAWS" section, the actual alignment can be obtained as follows:

    +

    1) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 2) String jobId = msaws.align(fastalist);
    + 3) Alignment alignment = msaws.getResult(jobId);

    +

    Line one loads FASTA sequence from the file
    + Line two submits them to web service represented by msaws proxy
    + Line three retrieves the alignment from a web service. This line will block the execution until the result is available. Use this with caution. In general, you should make sure that the calculation has been completed before attempting retrieving results. This is to avoid keeping the connection to the server on hold for a prolonged periods of time. While this may be ok with your local server, our public server (www.compbio.dundee.ac.uk/jabaws) will not let you hold the connection for longer than 10 minutes. This is done to prevent excessive load on the server. The next section describes how to check the status of the calculation.
    + Methods and classes mentioned in the excerpt are available from the JABAWS client library.

    +

    Checking the status of the calculation

    +

    You may have noticed that there was no pause between submitting the job and retrieving of the results. This is because getResult(jobId) method block the processing until the calculation is completed. However, taking into account that the connection holds server resources, our public server (www.compbio.dundee.ac.uk/jabaws) is configured to reset the connection after 10 minutes of waiting. To work around the connection reset you are encouraged to check whether the calculation has been completed before accessing the results. You can do it like this:

    +

    while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
    +     Thread.sleep(2000); // wait two seconds, then recheck the status
    + }

    +

    Aligning with presets

    +

    1) PresetManager presetman = msaws.getPresets();
    + 2) Preset preset = presetman.getPresetByName(presetName);
    + 3) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 4) String jobId = msaws.presetAlign(fastalist, preset);
    + 5) Alignment alignment = msaws.getResult(jobId);

    +

    Line one obtains the lists of presets supported by a web service.
    + Line two return a particular Preset + by its name
    + Lines three to five are doing the same job as in the first aligning sequences example.

    +

    Aligning with custom parameters

    +

    1) RunnerConfig options = msaws.getRunnerOptions();
    + 2) Argument matrix = options.getArgument("MATRIX");
    + 3) matrix.setValue("PAM300");
    + 4) Argument gapopenpenalty = options.getArgument("GAPOPEN");
    + 5) gapopenpenalty.setValue("20");
    + 6) List<Argument> arguments = new ArrayList<Argument>();
    + 7) arguments.add(matrix); + arguments.add(gapopenpenalty);
    + 8) List<FastaSequence> fastalist = SequenceUtil.readFasta(new FileInputStream(file));
    + 9) String jobId = msaws.customAlign(fastalist, arguments);
    + 10) Alignment alignment = msaws.getResult(jobId);

    +

    Line one obtains the RunnerConfig object that holds information on supported parameters and their values
    + Line two retrieve a particular parameter from the holder by its name
    + Lines three sets a value to this parameter which will be used in the calculation.
    + Line four and five do the same but for another parameter
    + Line 6 makes a List to hold the parameters
    + Line seven puts the parameters into that list
    + Line eight + and ten is the same as in previous examples
    + Line nine submit an alignment request with the sequences and the parameters
    + The names of all the parameters supported by a web service e.g. "PAM300" can be obtained using options.getArguments() method. Further details on the methods available from RunnerConfig object are available from the javadoc.

    +

    Writing alignments to a file

    +

    There is a utility method in the client library that does exactly that.

    +

    Alignment alignment = align(...)
    + FileOutputStream outStream = new FileOutputStream(file);
    + ClustalAlignmentUtil.writeClustalAlignment(outStream, align);

    +

    A complete client example

    +

    Finally, a complete example of the program that connects to JABAWS Clustal service and aligns sequences using one of the Clustal web service preset. Three is also a PDF version of this example with syntax highlighted. The text comments are commented by block style comments e.g. /* comment */, the alternatives given in the code are line commented // comment. You may want to remove line style comments to test alternatives of the functions. All you need for this to work is a JABAWS binary client. Please make sure that the client is in the Java class path before running this example.

    +
    +import java.io.ByteArrayInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.URL;
+import java.util.List;
+
+import javax.xml.namespace.QName;
+import javax.xml.ws.Service;
+
+import compbio.data.msa.MsaWS;
+import compbio.data.sequence.Alignment;
+import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.SequenceUtil;
+import compbio.metadata.JobSubmissionException;
+import compbio.metadata.LimitExceededException;
+import compbio.metadata.Preset;
+import compbio.metadata.PresetManager;
+import compbio.metadata.ResultNotAvailableException;
+import compbio.metadata.UnsupportedRuntimeException;
+import compbio.metadata.WrongParameterException;
+
+public class Example {
+
+	/*
+	 * Input sequences for alignment
+	 */
+	static final String input = ">Foo\r\n"
+			+ "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGR"
+			+ "VRWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDAGQAEAAAAAYTRAHQLLPEEPYITAQ"
+			+ "LLNWRRRLCDWRALDVLSAQVRAAVAQGVGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPL"
+			+ "APTRVRSKGPLRVGFVSNGFGAHPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQA"
+			+ "STLHDVTALGHLATAKHIRHHGIDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMD"
+			+ "YVLGDAFALPPALEPFYSEHVLRLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLN"
+			+ "PQSMARMLAVLREVPDSVLWLLSGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHAD"
+			+ "LFLDTHPYNAHTTASDALWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALAS"
+			+ "DPAALTALHARVDVLRRESGVFEMDGFADDFGALLQALARRHGWLGI\r\n"
+			+ "\r\n"
+			+ ">Bar\r\n"
+			+ "MGDTTAGEMAVQRGLALHQQRHAEAAVLLQQASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAH"
+			+ "QLLPEEPYITAQLLNAVAQGVGAVEPFAFLSEDASAAESVRPLAPTRVRSKGPLRVGFVSNGFGA"
+			+ "HPTGLLTVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHG"
+			+ "IDLLFDLRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVL"
+			+ "RLQGAFQPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLL"
+			+ "SGPGEADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGC"
+			+ "PVLTTPGETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESGV"
+			+ "FEMDGFADDFGALLQALARRHGWLGI\r\n"
+			+ "\r\n"
+			+ ">Friends\r\n"
+			+ "MTADGPRELLQLRAAVRHRPQDVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAVARLGRV"
+			+ "RWTQQRHAEAAVLLQQASDAAPEHPGIALWLGHALEDHQLLPEEPYITAQLDVLSAQVRAAVAQG"
+			+ "VGAVEPFAFLSEDASAAEQLACARTRAQAIAASVRPLAPTRVRSKGPLRVGFVSNGFGAHPTGLL"
+			+ "TVALFEALQRRQPDLQMHLFATSGDDGSTLRTRLAQASTLHDVTALGHLATAKHIRHHGIDLLFD"
+			+ "LRGWGGGGRPEVFALRPAPVQVNWLAYPGTSGAPWMDYVLGDAFALPPALEPFYSEHVLRLQGAF"
+			+ "QPSDTSRVVAEPPSRTQCGLPEQGVVLCCFNNSYKLNPQSMARMLAVLREVPDSVLWLLSGPGEA"
+			+ "DARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDALWTGCPVLTTP"
+			+ "GETFAARVAGSLNHHLGLDEMNVADDAAFVAKAVALASDPAALTALHARVDVLRRESI";
+
+	public static void main(String[] args) throws UnsupportedRuntimeException,
+			LimitExceededException, JobSubmissionException,
+			WrongParameterException, FileNotFoundException, IOException,
+			ResultNotAvailableException, InterruptedException {
+
+		String qualifiedServiceName = "http://msa.data.compbio/01/01/2010/";
+
+		/* Make a URL pointing to web service WSDL */
+		URL url = new URL(
+				"http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl");
+
+		/*
+		 * If you are making a client that connects to different web services
+		 * you can use something like this:
+		 */
+		// URL url = new URL(host + "/" + Services.ClustalWS.toString() +
+		// "?wsdl");
+
+		QName qname = new QName(qualifiedServiceName, "ClustalWS");
+		Service serv = Service.create(url, qname);
+		/*
+		 * Multiple sequence alignment interface for Clustal web service
+		 * instance
+		 */
+		MsaWS msaws = serv.getPort(new QName(qualifiedServiceName, "ClustalWS"
+				+ "Port"), MsaWS.class);
+
+		/* Get the list of available presets */
+		PresetManager presetman = msaws.getPresets();
+
+		/* Get the Preset object by preset name */
+		Preset preset = presetman
+				.getPresetByName("Disable gap weighting (Speed-oriented)");
+
+		/*
+		 * Load sequences in FASTA format from the file You can use something
+		 * like new FileInputStream(<filename>) to load sequence from the file
+		 */
+		List<FastaSequence> fastalist = SequenceUtil
+				.readFasta(new ByteArrayInputStream(input.getBytes()));
+
+		/*
+		 * Submit loaded sequences for an alignment using preset. The job
+		 * identifier is returned by this method, you can retrieve the results
+		 * with it sometime later.
+		 */
+		String jobId = msaws.presetAlign(fastalist, preset);
+
+		/* This method will block for the duration of the calculation */
+		Alignment alignment = msaws.getResult(jobId);
+
+		/*
+		 * This is a better way of obtaining results, it does not involve
+		 * holding the connection open for the duration of the calculation,
+		 * Besides, as the University of Dundee public server will reset the
+		 * connection after 10 minutes of idling, this is the only way to obtain
+		 * the results of long running task from our public server.
+		 */
+		// while (msaws.getJobStatus(jobId) != JobStatus.FINISHED) {
+		// Thread.sleep(1000); // wait a second, then recheck the status
+		// }
+
+		/* Output the alignment to standard out */
+		System.out.println(alignment);
+
+		// Alternatively, you can record retrieved alignment into the file in
+		// ClustalW format
+
+		// ClustalAlignmentUtil.writeClustalAlignment(new FileOutputStream(
+		// "output.al"), alignment);
+
+	}
+}
+
    +For a more detailed description of all available types and their functions please refer to the data model javadoc. +

    Building web services artifacts

    +

    JABAWS are the standard JAX-WS SOAP web services, which are WS-I basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as it provides a handful of useful methods in addition to plain data types.

    +

    wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl

    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/man_servervm.html b/website/man_servervm.html new file mode 100644 index 0000000..976d311 --- /dev/null +++ b/website/man_servervm.html @@ -0,0 +1,167 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    JABAWS Server Virtual Appliance

    + + +

    Troubleshooting

    + +

    What is JABAWS Server Virtual Appliance?

    +

    The JABAWS Server Virtual Appliance is an installation of JABAWS Web Application Archive (WAR) with all dependencies on TurnKey Linux within a Virtual Machine. The JABAWS virtual appliance is a way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. + + + All JABAWS clients, such as Jalview can be easily configured to use the appliance. + You can run the appliance with freely available VMWare Player or Oracle VirtualBox which you must install first. We have tested JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and VirtualBox v 3.2.12 on Windows, Linux and Mac. + However, you are not limited to these virtualization systems and can use JABAWS appliance with any commercial alternative.

    +

    When to use the virtual appliance

    +

    The appliance best suits users who would like to use the JABA web services locally, without an Internet connection, want to keep their data private +or uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users too. However, they can always deploy a JABAWS Server WAR distribution instead.
    +The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. If you thinking of running the JABAWS server for many users and want JABAWS to use a cluster for calculations you need a WAR version of JABAWS server instead. Virtual Appliance would not be the best option for that.

    + +

    How to install VMWare Player or VirtualBox

    +

    Please see the VMware Player +and Oracle VirtualBox web sites for up to date instructions and downloads.

    + +

    VMware Player appliance configuration

    +

    The free VMware Player can be used to run the JABAWS services from the Windows and Linux host operating systems, there is no support for Mac at the time of writing (December 2010). +However, VMware Fusion, a commercial VMware product, offers virtual machine support for Mac computers too.

    +

    To run the JABAWS server on VMware player, unpack the JABAWS VM into one of the folders on your local hard drive. Open VMware Player, click "Open Virtual Machine" and point the Player to the location of the JABAWS, then choose the JABAWS.vmx file to open an appliance.

    +

    When you play the machine for the first time the Player might ask you whether "This virtual machine may have been moved or copied.", say that you have copied it. That is all.

    +

    VirtualBox appliance configuration

    +

    VirtualBox can be used to run JABAWS services from Windows, Linux, Solaris or Mac host operating systems. Use the VitualBox "Import Appliance" option to import the JABAWS. Please bear in mind that to benefit from multiple CPU support under the VirtualBox software you need to enable hardware virtualization extensions, such as Intel Virtualization VT-x or AMD-V support in the BIOS of your computer. Unfortunately, we were unable to find a reliable way to do it on Mac, so some Macs running VirtualBox will be limited to one CPU only, irrespective of the number of CPUs of the host machine.

    +

    We found that, by default, virtualization extensions are enabled in VirtualBox irrespective of whether your computer supports them. You will get the VERR_VMX_MSR_LOCKED_OR_DISABLED exception if your computer does not support the extensions or their support is disabled. Just deselect the checkboxes shown on the screen shot below to solve the problem.

    +

    VirtualBox JABAWS VM configuration screen shot displaying virtualization settings.

    +

    VT-x extension on VirtualBox

    +

    JABAWS Appliance details

    +

    By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.

    +

    The VMware Player screen shot below displays JABAWS VM CPU settings.

    +

    vmware cpu settings

    + +

    JABAWS appliance configuration:

    +

    VMware info
    + - CPUs : 1
    + - RAM : 512 MB
    + - Networking : Host only (the VM has no access to the outside network, nothing from the outside network can access the VM)
    + - Hard disk : 20 GB (expanding)
    + - VMware tools : Installed

    +

    OS info
    + - OS : TurnKey Linux, based on Ubuntu 8.0.4 JEOS (Just-Enough-Operation-System)
    + - Installation : Oracle Java 6, Tomcat 6, JABAWS v. 1.0
    + - Hostname : tomcat
    + - IPv4 address : dhcp
    + - IPv6 address : auto
    + - DNS name : none
    + - Name server : dhcp
    + - Route : dhcp
    + - Keyboard : US_intl

    +

    Login credentials
    + - Root password: jabaws

    +

    Services

    +
      +
    • Default virtual console Alt+F7
      • +
    • Tomcat web server.
      + Access: http://VM_IP
      • +
    • JABAWS URL: http://VM_IP/jabaws
      • +
    • Web Shell
      + Access: https://VM_IP:12320/
      • +
    • Webmean
      + Access: https://VM_IP:12321/
      • +
    • SSH/SFTP
      + Access: root@VM_IP
      • +
    +

    Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. Under VirtualBox host only networking, first VM may have 192.168.56.101 IP address.

    +

    Configuring Jalview to work with your JABAWS VM

    +

    After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview help pages.

    +

    JABAWS welcome screen

    +

    If you click on Advanced Menu, you will see the configuration console, similar to the one below.

    +

    JABAWS welcome screen

    +

    If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.

    +

    VM Network Settings

    +

    By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)

    +

    VirtualBox fails to open the VM due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception

    +

    VERR_VMX_MSR_LOCKED_OR_DISABLED exception means that Intel Virtualization technology is disabled or not supported by your computer. If you have such a problem, please make sure you have configured the JABAWS VM with 1 CPU and disabled VT-X extensions. Alternatively you can enable virtualization extensions ion from the BIOS of your computer. Unfortunately, we cannot give you exact instructions on how to do this, as this would depend on your computer BIOS manufacturer. For MACs it may not be possible at all.

    +

    VirtualBox 4.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception

    +

    There were reports that VirtualBox version 4.0 suffers from this problem at least on Windows XP. The fix is to use the previous version of VirtualBox 3.2.12

    +

    VMWare Player fails to open the VM with "Fail to query source for information" exception

    +

    At the time of writing, the latest version of VMware Player 3.1.2 supported only a legacy OVF version 0.9. Whereas OVF packaged with JABAWS VM is version 1.0. Please use VMX - VMware specific configuration file with all VMware products.

    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/man_serverwar.html b/website/man_serverwar.html new file mode 100644 index 0000000..5d092e0 --- /dev/null +++ b/website/man_serverwar.html @@ -0,0 +1,264 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) Server Web Aplication aRchive manual + + + + + +
    + + +
    + + + +
    +

    JABAWS MANUAL

    + +

    JABAWS Server Web Application aRchive (WAR)

    + +

    Troubleshooting

    + +

    System Requirements

    +

    JABAWS requires a Java web application server compliant with +version 2.4 of the Java Servlet specification, and a Java 6 runtime +environment. We recommend using an official Oracle Java 6 runtime +environment, and Apache-Tomcat web application server version 6, but other versions may work as well.

    + +

    JABAWS Web Application aRchive can run on any host operating system that supports Java. However JABAWS depends on the third party programs which are not available for all operating systems. In particular, only Clustal and Muscle are currently available for MS Windows platform. + +

    +

    JABAWS comes with pre-compiled MS Windows and Linux IA32 binaries and contains all the binaries sources.

    +

    To run JABAWS on the cluster you must have shared disk space accessible from all cluster nodes.

    +

    Installing the JABAWS WAR file

    +

    JABAWS is distributed as a web application archive (WAR). To +deploy JABAWS in Apache-Tomcat - simply drop the war file into the +webapps directory of a running +Tomcat, and it will do the rest. If you used this deployment procedure, do not remove jabaws war file, otherwise Tomcat will undeploy your application!

    +

    For any other web application + server, please follow your server's specific deployment procedure + for 'WAR' files. If you install JABAWS on a MS Windows machine, then + at this point your JABAWS installation will already be up and + running, and you can try its services out as described here. If you install JABAWS on Linux you will need to set an executable flag for binaries. This is described here. If your host operating system is different from Windows or Linux then read on.

    +

    Preparing executables for use with JABAWS

    + +

    JABAWS's web services use command line programs to do +the actual analysis, so it must have access to programs +which can be executed on your platform. The native executables +bundled with JABAWS for Windows (32-bit) and Linux (i386, 32-bit) should be +OK for those systems. The source code for these +programs is also provided so you can recompile for your own +architecture and exploit any optimizations that your system can +provide. Alternately, if you have already got binaries on your +system, then you can simply change the paths in JABAWS's +configuration files so these are used instead.

    + +

    Using the pre-compiled i386 binaries on Linux

    + +

    Before the binaries that are bundled with JABAWS can be used, +they must first be made executable using the provided 'setexecflag.sh' script:

    + +
      +
    1. cd to <webapplicationpath>/binaries/src
      2. + +
    2. run sh setexecflag.sh
      3. + +
    3. Make sure binaries supplied work under your OS.
      + For this run each binary, without any command line options or +input files. If you see an error message complaining about missing +libraries or other problems, then you probably need to recompile the binaries. with
      4. + +
    4. Restart the Tomcat.
      5. +
    + +That's it! JABAWS should work at this point. Try it out using the JABAWS test client. If not, +read on... or have a look at deploying on Tomcat tips.
    + Note: You may want to enable logging, as described here.
    + + +

    Recompiling the bundled +programs for your system

    + +

    If you have a fully equipped build environment on your +(POSIX-like) system, then you should be able to recompile the +programs from the source distributions which are included +in the JABAWS war file. A script called 'compilebin.sh' is provided +to automate this task.

    + +
      +
    1. In a terminal window, change the working directory to binaries/src
      2. + +
    2. execute the compilebin.sh +script,
      + either use: chmod +x compilebin.sh; +compilebin.sh > compilebin.out;
      + or: sh compilebin.sh > +compilebin.out
      3. + +
    3. Now run sh setexecflag.sh
      + If any of the binaries was not recompiled, then a 'file not found' +error will be raised.
      4. + +
    4. Finally, restart your Tomcat server (or JABAWS application only), and test JABAWS to +check that it can use the new binaries.
      5. +
    + +

    If you couldn't compile everything, then it may be that your system does +not have all the tools required for compiling the programs. At the very +least check that you have gcc, g++ and make installed in your +system. If not install these packages and repeat the compilation +steps again. You should also review the compilebin.sh output - +which was redirected to compilebin.out, and any errors output to +the terminal. Finally, try obtaining the pre +compiled binaries for your OS.

    + +

    Reuse the binaries that are +already in your system

    + +

    If you would like to use the binaries you already have then you +just need to let JABAWS know there they are. To do this, edit: +conf/Executable.properties

    +

    When specifying paths to executables that already exist on your system, make sure you provide an absolute path, or one relative to the JABAWS directory inside webapps. For example, the default path for clustalw is defined +aslocal.clustalw.bin=binaries/src/clustalw/src/clustalw2 +Alternatively, instead of changing Executable.properties you could also replace +the executables bundled with JABAWS with the ones that you have, or make symbolic links to them. +Then the default configuration will work for you. More information +about the +Executable.properties file is given in the JABAWS Configuration chapter.

    + +

    Obtaining alignment +programs for your operating system

    + +

    You could search for pre-packaged compiled executable in your +system package repository or alternately, download pre-compiled +binaries from each alignment program's home page. Then, either +replace the executables supplied with the downloaded ones, or +modify the paths in executable.properties as described above. Below are some suggestions on where you may be able to get the binaries for your system.

    + +

    Testing JABAWS Server

    +

    First of all make sure that Tomcat server is started successfully. If this was the case, then you should see JABAWS home page when you navigate to your Tomcat JABAWS context path e.g. http://myhost.compbio.ac.uk:8080/jabawsIf you see it, then it is time to make sure that web services are working too. Assuming that you have unpacked/deployed JABAWS from the server war file, you should be able to navigate to the test program which can be found in <webapplicationpath>/WEB-INF/lib/jabaws-client.jar file. To run the tests type: java -jar jabaws-client.jar -h=<Your web application server host name, port and JABAWS context path>

    +

    For example to test all JABAWS web services on host myhost.compbio.ac.uk type:

    +

    java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws

    +

    You can choose a particular web server using -s option like this java -jar jabaws-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=ClustalWS This command line assumes that java executable is in your path and jabaws-client.jar is located in the current directory.

    +

    An example of the report testing tool produces for operating web service looks like this:

    +

    Connecting to service MuscleWS on http://myhost.compbio.ac.uk:8080/jabaws ... OK
    + Testing alignment with default parameters:
    + Queering job status...OK
    + Retrieving results...OK
    + Testing alignment with presets:
    + Aligning with preset 'Protein alignment(Fastest speed)'... OK
    + Aligning with preset 'Nucleotide alignment(Fastest speed)'... OK
    + Aligning with preset 'Huge alignments (speed-oriented)'... OK
    + Queering presets...OK
    + Queering Parameters...OK
    + Queering Limits...OK
    + Queering Local Engine Limits...OK
    + Check is completed service MuscleWS IS WORKING    An example of the response of a web service which is deployed but is not operating is below:

    +

    Connecting to service ProbconsWS on http://localhost:8080/ws ... OK
    + Testing alignment with default parameters:FAILED
    + Service ProbconsWS IS NOT FUNCTIONAL    If the web server did not respond the message looks like following: Connecting to service TcoffeeWS on http://localhost:8080/ws ... FAILED

    +

    Running many JABAWS instances on the same server

    +

    JABAWS is supplied as a Web Application aRchive which can be dealt with as any other web applications. So it is perfectly possible to run two JABAWS instances from the same server. Just make two different contexts on your application server and unpack JABAWS in both of them. For example if your server name is http://www.align.ac.uk, and the context names are public and private. Than one group of users could be given a URL http://www.align.ac.uk/public and another http://www.align.ac.uk/private. These contexts will be served by two independent JABAWS instances, and could be configured differently. If you keep local engine enabled, make sure you reduce the number of threads local engine is allowed to use to avoid overloading the server. Alternatively two completely separate web application server instances (e.g. Apache-Tomcat) could be used. This will give you a better resilience and more flexibility in memory settings.

    +

    JABAWS on a single server

    +

    You can run JABAWS on a single server. Obviously the capacity will be limited, but may be sufficient for a small lab. Installed on a single server, JABAWS executes tasks in parallel, so the more cores the server has the more requests it will be able to handle.

    +

    JABAWS supported cluster batch management systems

    +

    JABAWS uses DRMAA v. 1.0 library to send and manage jobs on the cluster. DRMAA supports many different cluster job management systems. Namely Sun Grid Engine, Condor, PBS, GridWay, Globus 2/4, PBSPro, LSF. For up to date information please consult DRMAA web site. We found that DRMAA implementation differ from platform to platform and were trying to use only the basic functions. We have only tested JABAWS on Sun Grid Engine v 6.2. Please let use know if you have any experience of running JABAWS on other platforms.

    +

    Manually deploying JABAWS application on Apache-Tomcat

    +

    To stop Tomcat from automatically undeploying your application if the war file is removed use an explicit application descriptor. It could come in different flavors, the one I prefer if to drop a context descriptor file into <tomcatRoot>conf/Catalina/localhost directory. Name your context file the same as your application folder e.g. if you JABAWS resides in webappl/jabaws folder, then call the context file jabaws.xml. Below is an example of content this file might have.

    +

    <?xml version="1.0" encoding="UTF-8"?>
    + <Context antiResourceLocking="false" privileged="true" />

    +

    This should be sufficient to prevent Tomcat from removing your JABAWS from WEBAPPS. For more information about the Tomcat deployer read this documentation on the Apache-Tomcat web site.

    +

    Apache-Tomcat fails to deploy jaba.war file

    +
      +
    • Make sure Tomcat have sufficient access rights to read your war file.
      • +
    • Restart the Tomcat, sometimes it will not since that the new war file is added without restart
      • +
    • If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.
      • +
    +
    + + + +
    + + +
    + + + + + + + + diff --git a/website/manual.html b/website/manual.html new file mode 100644 index 0000000..a012c5a --- /dev/null +++ b/website/manual.html @@ -0,0 +1,116 @@ + + + + +Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started + + + + + + +
    + +
    + + +
    + +

    JABAWS MANUAL

    +

    Quick Start Guide

    + +

    Choose JABAWS distribution

    +

    There are three main packages you could use

    +
      +
    1. A JABAWS Server Virtual Appliance (or Virtual Machine) - for anyone who wants to run JABAWS locally for themselves
      2. +
    2. A JABAWS Server Web Application Archive (WAR) package - for anyone who wants to run JABAWS for their group, lab or organization. Wants to use the cluster or perform very large tasks
      3. +
    3. A client package - for anyone who wants to use JABAWS from their own code, without Jalview, scripting against local or public version of JABAWS Server.
      4. +
    +

    Virtual Appliance (VA) package (1) contains TurnKey Linux with JABAWS installed. JABAWS VA contains JABAWS WAR deployed on the Apache Tomcat 6 web application server. If you use MS Windows read no further - the VA is the way to go. You would need to install VMWare Player or Oracle VirtualBox (both are free) on your computer to use this package. More details about JABAWS virtual appliance is available from the Server VA section of the manual.

    +

    Option 2, Web Application Archive package contains JABAWS ready to be deployed on the Servlet 2.4 compatible web application server such as Apache Tomcat version 6. To make this version work you would need

    +
      +
    1. Install Apache-Tomcat or similar web application server.
      2. +
    2. If you are not on Linux, you would have to make binaries for your system available to JABAWS.
      3. +
    +

    Read more on JABAWS WAR in the manual.

    +

    A client only package (3) contains the JABAWS command line client. It functionality is equivalent to that of Jalview . This is the package for anyone who wants to connect to and to use JABAWS from their own software. Read more about how to use command line client in the CMD Client section of the manual. Also, JABA Web Services are fully WS-I compliant, so one could use any language to access them.

    +

    If you chose option 1

    +

    and you work on Windows or Linux or Unix

    +
      +
    • download and install VMWare Player
      • +
    • Download JABAWS Virtual Appliance
      • +
    • Unpack JABAWS virtual appliance and open it with VMware Player.
      • +
    +

    otherwise

    +
      +
    • download and install Virtual Box.
      • +
    • Download JABAWS Virtual Appliance
      • +
    • Unpack JABAWS virtual appliance, import it into VirtualBox and then start the appliance.
      • +
    +

    If you chose option 2

    +

    If you are on Linux or Windows

    +
    1. Download JABAWS WAR
      2. +
    2. Download and install Apache-Tomcat
      3. +
    3. Drop the JABAWS war file into tomcat/webapps directory.
      4. +
    4. If you are on Linux, cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script to set an executable flag for JABAWS binaries.
      5. +
    5. Restart the Tomcat
      6. +
    +

    otherwise

    +
      +
    • Complete steps 1-3 from the above.
      • +
    • cd to webapps/jabaws/binaries/src/ and execute ./compilebin.sh script to compile all binaries JABAWS depends on.
      • +
    • cd to webapps/jabaws/binaries/src/ and execute ./setexecflag.sh script.
      • +
    • Restart the Tomcat
      • +
    +

    Once you have JABAWS working you can point the Jalview to your local JABAWS.

    +
      +
    • Download and start the desktop version of Jalview
      • +
    • Go to Jalview->Tools->Preferences->Webservices->New Service URL and enter the JABAWS URL which you can see one your appliance is booted up.
      • +
    +

    if you chose option 3

    +

    You can use the client straight out of the box.

    +
    + +
    + + +
    + + + + + + + + diff --git a/website/print.css b/website/print.css new file mode 100644 index 0000000..4f6e7b8 --- /dev/null +++ b/website/print.css @@ -0,0 +1,188 @@ + +#banner { background:none !important; color:#000000 !important; text-align:center; } + +#panel { display:none !important } + +#content { margin:0.5em; border-bottom:solid 1px #6994af; } + +#page { margin: 0.5em; } + +#wrapper { background:none; } + +ul { + list-style-type: circle; +} + + +#panel a:link, a:visited { + text-decoration: none; + display:block; + line-height: 1em; + padding:10px; + color:#000000; + text-decoration:none; + } + +#panel a:hover { + background-color: transparent; + text-decoration: underline; + } + + +strong { + font-weight:bold; + color:#003366; +} + +pre { + font-family:Arial, Helvetica, sans-serif; +} + +p { + line-height: 1.4em; +} + +.hightlight { +font-style:italic; +font-family:"Courier New", Courier, monospace; +} + +.code { + font-size-adjust:0.4; + color:black; + background-color:#F5F5F5; + font-family:"Courier New",Courier,monospace; + font-style:normal; + margin:1em 0; + padding: 0.5em; + border: 1px dashed black; +} + + +.box { + font-size-adjust:0.5; + color:black; + background-color:#F5F5F5; + font-family:Arial, Helvetica, sans-serif; + font-style:normal; + margin:1em 0; + padding: 0.5em; + border: 1px solid black; + display:block; +} + +.u { text-decoration: underline; } +.headeru { text-shadow: black 0.05em 0.05em 0.01em ;} + +/* Table styles */ +table { + border-collapse: collapse; + border: 1px solid #666; + margin: 20px 0 20px 0; + width: 100%; +} +th, td { + margin: 2px 4px 2px 4px; + padding: 0 5px; + text-align: left; + vertical-align: top; + border: 1px solid #666; +} + +table caption { + font: 1.5em Georgia, "Times New Roman", Times, serif; + padding: 1em; + background-color: #9c9; +} + +.mainheader { + font: 1.5em Georgia, "Times New Roman", Times, serif; + background-color: #9c9; + text-align:center; + line-height:1em; +} + +tr { + background-color: #eee; +} + +tr:nth-child(odd) { + background-color: #ccc; +} + + +span.directory { +background: transparent url(images/dir.gif) no-repeat scroll left center; +color:#666666; +font-family:"Courier New",Courier,monospace; +font-style:normal; +padding:0 0 0 15px; +} + +.attention { +color:#993333; +} + +.source { + border:1px solid #858789; + display:block; + margin:26px 0; + overflow:visible; +} + +/* OPEN state styles */ +.source .body { + background:#F5F5F5 none repeat scroll right 0; + color:#434546; + padding:7px 15px; +/* white-space:pre-wrap; */ + word-wrap:break-word; +} + +.source .header { + background:#E9EAEC url(images/minus.png) no-repeat scroll 98% center; + color:#3B3D3F; + cursor:pointer; + font-weight:bold; + height:30px; + line-height:30px; + padding:0 0 0 15px; +} + +/* CLOSED state styles */ +.source .body.collapsed { + display:block !important; +} + +.source .header.collapsed { + background:#E9EAEC url(images/plus.png) no-repeat scroll 98% center; + padding:0 15px 0 15px; +} + +#copyright { text-align:right; + color:#999999; + font-family:Verdana, Arial, Helvetica, sans-serif; + font-size:smaller; + line-height:1em; + } + +.body .code { + margin:0; + padding:0; + border:0; + font-family:"Courier New",Courier,monospace; + font-style:normal; +} + +body { + font-family:Arial, Helvetica, sans-serif; + font-size: 9pt; + background-color: white; + line-height: 2em; +} + +h3 {border-bottom: 1px solid grey; margin-top: 2em; } + +#headtitle { margin:0; text-align:center; color:#003b62; font-weight:600;} + +h2 {margin:1.8em 0 0 0; color:#003b62; font-weight:600;} diff --git a/website/prototype-1.6.0.3.js b/website/prototype-1.6.0.3.js new file mode 100644 index 0000000..dfe8ab4 --- /dev/null +++ b/website/prototype-1.6.0.3.js @@ -0,0 +1,4320 @@ +/* Prototype JavaScript framework, version 1.6.0.3 + * (c) 2005-2008 Sam Stephenson + * + * Prototype is freely distributable under the terms of an MIT-style license. + * For details, see the Prototype web site: http://www.prototypejs.org/ + * + *--------------------------------------------------------------------------*/ + +var Prototype = { + Version: '1.6.0.3', + + Browser: { + IE: !!(window.attachEvent && + navigator.userAgent.indexOf('Opera') === -1), + Opera: navigator.userAgent.indexOf('Opera') > -1, + WebKit: navigator.userAgent.indexOf('AppleWebKit/') > -1, + Gecko: navigator.userAgent.indexOf('Gecko') > -1 && + navigator.userAgent.indexOf('KHTML') === -1, + MobileSafari: !!navigator.userAgent.match(/Apple.*Mobile.*Safari/) + }, + + BrowserFeatures: { + XPath: !!document.evaluate, + SelectorsAPI: !!document.querySelector, + ElementExtensions: !!window.HTMLElement, + SpecificElementExtensions: + document.createElement('div')['__proto__'] && + document.createElement('div')['__proto__'] !== + document.createElement('form')['__proto__'] + }, + + ScriptFragment: ']*>([\\S\\s]*?)<\/script>', + JSONFilter: /^\/\*-secure-([\s\S]*)\*\/\s*$/, + + emptyFunction: function() { }, + K: function(x) { return x } +}; + +if (Prototype.Browser.MobileSafari) + Prototype.BrowserFeatures.SpecificElementExtensions = false; + + +/* Based on Alex Arnell's inheritance implementation. */ +var Class = { + create: function() { + var parent = null, properties = $A(arguments); + if (Object.isFunction(properties[0])) + parent = properties.shift(); + + function klass() { + this.initialize.apply(this, arguments); + } + + Object.extend(klass, Class.Methods); + klass.superclass = parent; + klass.subclasses = []; + + if (parent) { + var subclass = function() { }; + subclass.prototype = parent.prototype; + klass.prototype = new subclass; + parent.subclasses.push(klass); + } + + for (var i = 0; i < properties.length; i++) + klass.addMethods(properties[i]); + + if (!klass.prototype.initialize) + klass.prototype.initialize = Prototype.emptyFunction; + + klass.prototype.constructor = klass; + + return klass; + } +}; + +Class.Methods = { + addMethods: function(source) { + var ancestor = this.superclass && this.superclass.prototype; + var properties = Object.keys(source); + + if (!Object.keys({ toString: true }).length) + properties.push("toString", "valueOf"); + + for (var i = 0, length = properties.length; i < length; i++) { + var property = properties[i], value = source[property]; + if (ancestor && Object.isFunction(value) && + value.argumentNames().first() == "$super") { + var method = value; + value = (function(m) { + return function() { return ancestor[m].apply(this, arguments) }; + })(property).wrap(method); + + value.valueOf = method.valueOf.bind(method); + value.toString = method.toString.bind(method); + } + this.prototype[property] = value; + } + + return this; + } +}; + +var Abstract = { }; + +Object.extend = function(destination, source) { + for (var property in source) + destination[property] = source[property]; + return destination; +}; + +Object.extend(Object, { + inspect: function(object) { + try { + if (Object.isUndefined(object)) return 'undefined'; + if (object === null) return 'null'; + return object.inspect ? object.inspect() : String(object); + } catch (e) { + if (e instanceof RangeError) return '...'; + throw e; + } + }, + + toJSON: function(object) { + var type = typeof object; + switch (type) { + case 'undefined': + case 'function': + case 'unknown': return; + case 'boolean': return object.toString(); + } + + if (object === null) return 'null'; + if (object.toJSON) return object.toJSON(); + if (Object.isElement(object)) return; + + var results = []; + for (var property in object) { + var value = Object.toJSON(object[property]); + if (!Object.isUndefined(value)) + results.push(property.toJSON() + ': ' + value); + } + + return '{' + results.join(', ') + '}'; + }, + + toQueryString: function(object) { + return $H(object).toQueryString(); + }, + + toHTML: function(object) { + return object && object.toHTML ? object.toHTML() : String.interpret(object); + }, + + keys: function(object) { + var keys = []; + for (var property in object) + keys.push(property); + return keys; + }, + + values: function(object) { + var values = []; + for (var property in object) + values.push(object[property]); + return values; + }, + + clone: function(object) { + return Object.extend({ }, object); + }, + + isElement: function(object) { + return !!(object && object.nodeType == 1); + }, + + isArray: function(object) { + return object != null && typeof object == "object" && + 'splice' in object && 'join' in object; + }, + + isHash: function(object) { + return object instanceof Hash; + }, + + isFunction: function(object) { + return typeof object == "function"; + }, + + isString: function(object) { + return typeof object == "string"; + }, + + isNumber: function(object) { + return typeof object == "number"; + }, + + isUndefined: function(object) { + return typeof object == "undefined"; + } +}); + +Object.extend(Function.prototype, { + argumentNames: function() { + var names = this.toString().match(/^[\s\(]*function[^(]*\(([^\)]*)\)/)[1] + .replace(/\s+/g, '').split(','); + return names.length == 1 && !names[0] ? [] : names; + }, + + bind: function() { + if (arguments.length < 2 && Object.isUndefined(arguments[0])) return this; + var __method = this, args = $A(arguments), object = args.shift(); + return function() { + return __method.apply(object, args.concat($A(arguments))); + } + }, + + bindAsEventListener: function() { + var __method = this, args = $A(arguments), object = args.shift(); + return function(event) { + return __method.apply(object, [event || window.event].concat(args)); + } + }, + + curry: function() { + if (!arguments.length) return this; + var __method = this, args = $A(arguments); + return function() { + return __method.apply(this, args.concat($A(arguments))); + } + }, + + delay: function() { + var __method = this, args = $A(arguments), timeout = args.shift() * 1000; + return window.setTimeout(function() { + return __method.apply(__method, args); + }, timeout); + }, + + defer: function() { + var args = [0.01].concat($A(arguments)); + return this.delay.apply(this, args); + }, + + wrap: function(wrapper) { + var __method = this; + return function() { + return wrapper.apply(this, [__method.bind(this)].concat($A(arguments))); + } + }, + + methodize: function() { + if (this._methodized) return this._methodized; + var __method = this; + return this._methodized = function() { + return __method.apply(null, [this].concat($A(arguments))); + }; + } +}); + +Date.prototype.toJSON = function() { + return '"' + this.getUTCFullYear() + '-' + + (this.getUTCMonth() + 1).toPaddedString(2) + '-' + + this.getUTCDate().toPaddedString(2) + 'T' + + this.getUTCHours().toPaddedString(2) + ':' + + this.getUTCMinutes().toPaddedString(2) + ':' + + this.getUTCSeconds().toPaddedString(2) + 'Z"'; +}; + +var Try = { + these: function() { + var returnValue; + + for (var i = 0, length = arguments.length; i < length; i++) { + var lambda = arguments[i]; + try { + returnValue = lambda(); + break; + } catch (e) { } + } + + return returnValue; + } +}; + +RegExp.prototype.match = RegExp.prototype.test; + +RegExp.escape = function(str) { + return String(str).replace(/([.*+?^=!:${}()|[\]\/\\])/g, '\\$1'); +}; + +/*--------------------------------------------------------------------------*/ + +var PeriodicalExecuter = Class.create({ + initialize: function(callback, frequency) { + this.callback = callback; + this.frequency = frequency; + this.currentlyExecuting = false; + + this.registerCallback(); + }, + + registerCallback: function() { + this.timer = setInterval(this.onTimerEvent.bind(this), this.frequency * 1000); + }, + + execute: function() { + this.callback(this); + }, + + stop: function() { + if (!this.timer) return; + clearInterval(this.timer); + this.timer = null; + }, + + onTimerEvent: function() { + if (!this.currentlyExecuting) { + try { + this.currentlyExecuting = true; + this.execute(); + } finally { + this.currentlyExecuting = false; + } + } + } +}); +Object.extend(String, { + interpret: function(value) { + return value == null ? '' : String(value); + }, + specialChar: { + '\b': '\\b', + '\t': '\\t', + '\n': '\\n', + '\f': '\\f', + '\r': '\\r', + '\\': '\\\\' + } +}); + +Object.extend(String.prototype, { + gsub: function(pattern, replacement) { + var result = '', source = this, match; + replacement = arguments.callee.prepareReplacement(replacement); + + while (source.length > 0) { + if (match = source.match(pattern)) { + result += source.slice(0, match.index); + result += String.interpret(replacement(match)); + source = source.slice(match.index + match[0].length); + } else { + result += source, source = ''; + } + } + return result; + }, + + sub: function(pattern, replacement, count) { + replacement = this.gsub.prepareReplacement(replacement); + count = Object.isUndefined(count) ? 1 : count; + + return this.gsub(pattern, function(match) { + if (--count < 0) return match[0]; + return replacement(match); + }); + }, + + scan: function(pattern, iterator) { + this.gsub(pattern, iterator); + return String(this); + }, + + truncate: function(length, truncation) { + length = length || 30; + truncation = Object.isUndefined(truncation) ? '...' : truncation; + return this.length > length ? + this.slice(0, length - truncation.length) + truncation : String(this); + }, + + strip: function() { + return this.replace(/^\s+/, '').replace(/\s+$/, ''); + }, + + stripTags: function() { + return this.replace(/<\/?[^>]+>/gi, ''); + }, + + stripScripts: function() { + return this.replace(new RegExp(Prototype.ScriptFragment, 'img'), ''); + }, + + extractScripts: function() { + var matchAll = new RegExp(Prototype.ScriptFragment, 'img'); + var matchOne = new RegExp(Prototype.ScriptFragment, 'im'); + return (this.match(matchAll) || []).map(function(scriptTag) { + return (scriptTag.match(matchOne) || ['', ''])[1]; + }); + }, + + evalScripts: function() { + return this.extractScripts().map(function(script) { return eval(script) }); + }, + + escapeHTML: function() { + var self = arguments.callee; + self.text.data = this; + return self.div.innerHTML; + }, + + unescapeHTML: function() { + var div = new Element('div'); + div.innerHTML = this.stripTags(); + return div.childNodes[0] ? (div.childNodes.length > 1 ? + $A(div.childNodes).inject('', function(memo, node) { return memo+node.nodeValue }) : + div.childNodes[0].nodeValue) : ''; + }, + + toQueryParams: function(separator) { + var match = this.strip().match(/([^?#]*)(#.*)?$/); + if (!match) return { }; + + return match[1].split(separator || '&').inject({ }, function(hash, pair) { + if ((pair = pair.split('='))[0]) { + var key = decodeURIComponent(pair.shift()); + var value = pair.length > 1 ? pair.join('=') : pair[0]; + if (value != undefined) value = decodeURIComponent(value); + + if (key in hash) { + if (!Object.isArray(hash[key])) hash[key] = [hash[key]]; + hash[key].push(value); + } + else hash[key] = value; + } + return hash; + }); + }, + + toArray: function() { + return this.split(''); + }, + + succ: function() { + return this.slice(0, this.length - 1) + + String.fromCharCode(this.charCodeAt(this.length - 1) + 1); + }, + + times: function(count) { + return count < 1 ? '' : new Array(count + 1).join(this); + }, + + camelize: function() { + var parts = this.split('-'), len = parts.length; + if (len == 1) return parts[0]; + + var camelized = this.charAt(0) == '-' + ? parts[0].charAt(0).toUpperCase() + parts[0].substring(1) + : parts[0]; + + for (var i = 1; i < len; i++) + camelized += parts[i].charAt(0).toUpperCase() + parts[i].substring(1); + + return camelized; + }, + + capitalize: function() { + return this.charAt(0).toUpperCase() + this.substring(1).toLowerCase(); + }, + + underscore: function() { + return this.gsub(/::/, '/').gsub(/([A-Z]+)([A-Z][a-z])/,'#{1}_#{2}').gsub(/([a-z\d])([A-Z])/,'#{1}_#{2}').gsub(/-/,'_').toLowerCase(); + }, + + dasherize: function() { + return this.gsub(/_/,'-'); + }, + + inspect: function(useDoubleQuotes) { + var escapedString = this.gsub(/[\x00-\x1f\\]/, function(match) { + var character = String.specialChar[match[0]]; + return character ? character : '\\u00' + match[0].charCodeAt().toPaddedString(2, 16); + }); + if (useDoubleQuotes) return '"' + escapedString.replace(/"/g, '\\"') + '"'; + return "'" + escapedString.replace(/'/g, '\\\'') + "'"; + }, + + toJSON: function() { + return this.inspect(true); + }, + + unfilterJSON: function(filter) { + return this.sub(filter || Prototype.JSONFilter, '#{1}'); + }, + + isJSON: function() { + var str = this; + if (str.blank()) return false; + str = this.replace(/\\./g, '@').replace(/"[^"\\\n\r]*"/g, ''); + return (/^[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t]*$/).test(str); + }, + + evalJSON: function(sanitize) { + var json = this.unfilterJSON(); + try { + if (!sanitize || json.isJSON()) return eval('(' + json + ')'); + } catch (e) { } + throw new SyntaxError('Badly formed JSON string: ' + this.inspect()); + }, + + include: function(pattern) { + return this.indexOf(pattern) > -1; + }, + + startsWith: function(pattern) { + return this.indexOf(pattern) === 0; + }, + + endsWith: function(pattern) { + var d = this.length - pattern.length; + return d >= 0 && this.lastIndexOf(pattern) === d; + }, + + empty: function() { + return this == ''; + }, + + blank: function() { + return /^\s*$/.test(this); + }, + + interpolate: function(object, pattern) { + return new Template(this, pattern).evaluate(object); + } +}); + +if (Prototype.Browser.WebKit || Prototype.Browser.IE) Object.extend(String.prototype, { + escapeHTML: function() { + return this.replace(/&/g,'&').replace(//g,'>'); + }, + unescapeHTML: function() { + return this.stripTags().replace(/&/g,'&').replace(/</g,'<').replace(/>/g,'>'); + } +}); + +String.prototype.gsub.prepareReplacement = function(replacement) { + if (Object.isFunction(replacement)) return replacement; + var template = new Template(replacement); + return function(match) { return template.evaluate(match) }; +}; + +String.prototype.parseQuery = String.prototype.toQueryParams; + +Object.extend(String.prototype.escapeHTML, { + div: document.createElement('div'), + text: document.createTextNode('') +}); + +String.prototype.escapeHTML.div.appendChild(String.prototype.escapeHTML.text); + +var Template = Class.create({ + initialize: function(template, pattern) { + this.template = template.toString(); + this.pattern = pattern || Template.Pattern; + }, + + evaluate: function(object) { + if (Object.isFunction(object.toTemplateReplacements)) + object = object.toTemplateReplacements(); + + return this.template.gsub(this.pattern, function(match) { + if (object == null) return ''; + + var before = match[1] || ''; + if (before == '\\') return match[2]; + + var ctx = object, expr = match[3]; + var pattern = /^([^.[]+|\[((?:.*?[^\\])?)\])(\.|\[|$)/; + match = pattern.exec(expr); + if (match == null) return before; + + while (match != null) { + var comp = match[1].startsWith('[') ? match[2].gsub('\\\\]', ']') : match[1]; + ctx = ctx[comp]; + if (null == ctx || '' == match[3]) break; + expr = expr.substring('[' == match[3] ? match[1].length : match[0].length); + match = pattern.exec(expr); + } + + return before + String.interpret(ctx); + }); + } +}); +Template.Pattern = /(^|.|\r|\n)(#\{(.*?)\})/; + +var $break = { }; + +var Enumerable = { + each: function(iterator, context) { + var index = 0; + try { + this._each(function(value) { + iterator.call(context, value, index++); + }); + } catch (e) { + if (e != $break) throw e; + } + return this; + }, + + eachSlice: function(number, iterator, context) { + var index = -number, slices = [], array = this.toArray(); + if (number < 1) return array; + while ((index += number) < array.length) + slices.push(array.slice(index, index+number)); + return slices.collect(iterator, context); + }, + + all: function(iterator, context) { + iterator = iterator || Prototype.K; + var result = true; + this.each(function(value, index) { + result = result && !!iterator.call(context, value, index); + if (!result) throw $break; + }); + return result; + }, + + any: function(iterator, context) { + iterator = iterator || Prototype.K; + var result = false; + this.each(function(value, index) { + if (result = !!iterator.call(context, value, index)) + throw $break; + }); + return result; + }, + + collect: function(iterator, context) { + iterator = iterator || Prototype.K; + var results = []; + this.each(function(value, index) { + results.push(iterator.call(context, value, index)); + }); + return results; + }, + + detect: function(iterator, context) { + var result; + this.each(function(value, index) { + if (iterator.call(context, value, index)) { + result = value; + throw $break; + } + }); + return result; + }, + + findAll: function(iterator, context) { + var results = []; + this.each(function(value, index) { + if (iterator.call(context, value, index)) + results.push(value); + }); + return results; + }, + + grep: function(filter, iterator, context) { + iterator = iterator || Prototype.K; + var results = []; + + if (Object.isString(filter)) + filter = new RegExp(filter); + + this.each(function(value, index) { + if (filter.match(value)) + results.push(iterator.call(context, value, index)); + }); + return results; + }, + + include: function(object) { + if (Object.isFunction(this.indexOf)) + if (this.indexOf(object) != -1) return true; + + var found = false; + this.each(function(value) { + if (value == object) { + found = true; + throw $break; + } + }); + return found; + }, + + inGroupsOf: function(number, fillWith) { + fillWith = Object.isUndefined(fillWith) ? null : fillWith; + return this.eachSlice(number, function(slice) { + while(slice.length < number) slice.push(fillWith); + return slice; + }); + }, + + inject: function(memo, iterator, context) { + this.each(function(value, index) { + memo = iterator.call(context, memo, value, index); + }); + return memo; + }, + + invoke: function(method) { + var args = $A(arguments).slice(1); + return this.map(function(value) { + return value[method].apply(value, args); + }); + }, + + max: function(iterator, context) { + iterator = iterator || Prototype.K; + var result; + this.each(function(value, index) { + value = iterator.call(context, value, index); + if (result == null || value >= result) + result = value; + }); + return result; + }, + + min: function(iterator, context) { + iterator = iterator || Prototype.K; + var result; + this.each(function(value, index) { + value = iterator.call(context, value, index); + if (result == null || value < result) + result = value; + }); + return result; + }, + + partition: function(iterator, context) { + iterator = iterator || Prototype.K; + var trues = [], falses = []; + this.each(function(value, index) { + (iterator.call(context, value, index) ? + trues : falses).push(value); + }); + return [trues, falses]; + }, + + pluck: function(property) { + var results = []; + this.each(function(value) { + results.push(value[property]); + }); + return results; + }, + + reject: function(iterator, context) { + var results = []; + this.each(function(value, index) { + if (!iterator.call(context, value, index)) + results.push(value); + }); + return results; + }, + + sortBy: function(iterator, context) { + return this.map(function(value, index) { + return { + value: value, + criteria: iterator.call(context, value, index) + }; + }).sort(function(left, right) { + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; + }).pluck('value'); + }, + + toArray: function() { + return this.map(); + }, + + zip: function() { + var iterator = Prototype.K, args = $A(arguments); + if (Object.isFunction(args.last())) + iterator = args.pop(); + + var collections = [this].concat(args).map($A); + return this.map(function(value, index) { + return iterator(collections.pluck(index)); + }); + }, + + size: function() { + return this.toArray().length; + }, + + inspect: function() { + return '#'; + } +}; + +Object.extend(Enumerable, { + map: Enumerable.collect, + find: Enumerable.detect, + select: Enumerable.findAll, + filter: Enumerable.findAll, + member: Enumerable.include, + entries: Enumerable.toArray, + every: Enumerable.all, + some: Enumerable.any +}); +function $A(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + var length = iterable.length || 0, results = new Array(length); + while (length--) results[length] = iterable[length]; + return results; +} + +if (Prototype.Browser.WebKit) { + $A = function(iterable) { + if (!iterable) return []; + // In Safari, only use the `toArray` method if it's not a NodeList. + // A NodeList is a function, has an function `item` property, and a numeric + // `length` property. Adapted from Google Doctype. + if (!(typeof iterable === 'function' && typeof iterable.length === + 'number' && typeof iterable.item === 'function') && iterable.toArray) + return iterable.toArray(); + var length = iterable.length || 0, results = new Array(length); + while (length--) results[length] = iterable[length]; + return results; + }; +} + +Array.from = $A; + +Object.extend(Array.prototype, Enumerable); + +if (!Array.prototype._reverse) Array.prototype._reverse = Array.prototype.reverse; + +Object.extend(Array.prototype, { + _each: function(iterator) { + for (var i = 0, length = this.length; i < length; i++) + iterator(this[i]); + }, + + clear: function() { + this.length = 0; + return this; + }, + + first: function() { + return this[0]; + }, + + last: function() { + return this[this.length - 1]; + }, + + compact: function() { + return this.select(function(value) { + return value != null; + }); + }, + + flatten: function() { + return this.inject([], function(array, value) { + return array.concat(Object.isArray(value) ? + value.flatten() : [value]); + }); + }, + + without: function() { + var values = $A(arguments); + return this.select(function(value) { + return !values.include(value); + }); + }, + + reverse: function(inline) { + return (inline !== false ? this : this.toArray())._reverse(); + }, + + reduce: function() { + return this.length > 1 ? this : this[0]; + }, + + uniq: function(sorted) { + return this.inject([], function(array, value, index) { + if (0 == index || (sorted ? array.last() != value : !array.include(value))) + array.push(value); + return array; + }); + }, + + intersect: function(array) { + return this.uniq().findAll(function(item) { + return array.detect(function(value) { return item === value }); + }); + }, + + clone: function() { + return [].concat(this); + }, + + size: function() { + return this.length; + }, + + inspect: function() { + return '[' + this.map(Object.inspect).join(', ') + ']'; + }, + + toJSON: function() { + var results = []; + this.each(function(object) { + var value = Object.toJSON(object); + if (!Object.isUndefined(value)) results.push(value); + }); + return '[' + results.join(', ') + ']'; + } +}); + +// use native browser JS 1.6 implementation if available +if (Object.isFunction(Array.prototype.forEach)) + Array.prototype._each = Array.prototype.forEach; + +if (!Array.prototype.indexOf) Array.prototype.indexOf = function(item, i) { + i || (i = 0); + var length = this.length; + if (i < 0) i = length + i; + for (; i < length; i++) + if (this[i] === item) return i; + return -1; +}; + +if (!Array.prototype.lastIndexOf) Array.prototype.lastIndexOf = function(item, i) { + i = isNaN(i) ? this.length : (i < 0 ? this.length + i : i) + 1; + var n = this.slice(0, i).reverse().indexOf(item); + return (n < 0) ? n : i - n - 1; +}; + +Array.prototype.toArray = Array.prototype.clone; + +function $w(string) { + if (!Object.isString(string)) return []; + string = string.strip(); + return string ? string.split(/\s+/) : []; +} + +if (Prototype.Browser.Opera){ + Array.prototype.concat = function() { + var array = []; + for (var i = 0, length = this.length; i < length; i++) array.push(this[i]); + for (var i = 0, length = arguments.length; i < length; i++) { + if (Object.isArray(arguments[i])) { + for (var j = 0, arrayLength = arguments[i].length; j < arrayLength; j++) + array.push(arguments[i][j]); + } else { + array.push(arguments[i]); + } + } + return array; + }; +} +Object.extend(Number.prototype, { + toColorPart: function() { + return this.toPaddedString(2, 16); + }, + + succ: function() { + return this + 1; + }, + + times: function(iterator, context) { + $R(0, this, true).each(iterator, context); + return this; + }, + + toPaddedString: function(length, radix) { + var string = this.toString(radix || 10); + return '0'.times(length - string.length) + string; + }, + + toJSON: function() { + return isFinite(this) ? this.toString() : 'null'; + } +}); + +$w('abs round ceil floor').each(function(method){ + Number.prototype[method] = Math[method].methodize(); +}); +function $H(object) { + return new Hash(object); +}; + +var Hash = Class.create(Enumerable, (function() { + + function toQueryPair(key, value) { + if (Object.isUndefined(value)) return key; + return key + '=' + encodeURIComponent(String.interpret(value)); + } + + return { + initialize: function(object) { + this._object = Object.isHash(object) ? object.toObject() : Object.clone(object); + }, + + _each: function(iterator) { + for (var key in this._object) { + var value = this._object[key], pair = [key, value]; + pair.key = key; + pair.value = value; + iterator(pair); + } + }, + + set: function(key, value) { + return this._object[key] = value; + }, + + get: function(key) { + // simulating poorly supported hasOwnProperty + if (this._object[key] !== Object.prototype[key]) + return this._object[key]; + }, + + unset: function(key) { + var value = this._object[key]; + delete this._object[key]; + return value; + }, + + toObject: function() { + return Object.clone(this._object); + }, + + keys: function() { + return this.pluck('key'); + }, + + values: function() { + return this.pluck('value'); + }, + + index: function(value) { + var match = this.detect(function(pair) { + return pair.value === value; + }); + return match && match.key; + }, + + merge: function(object) { + return this.clone().update(object); + }, + + update: function(object) { + return new Hash(object).inject(this, function(result, pair) { + result.set(pair.key, pair.value); + return result; + }); + }, + + toQueryString: function() { + return this.inject([], function(results, pair) { + var key = encodeURIComponent(pair.key), values = pair.value; + + if (values && typeof values == 'object') { + if (Object.isArray(values)) + return results.concat(values.map(toQueryPair.curry(key))); + } else results.push(toQueryPair(key, values)); + return results; + }).join('&'); + }, + + inspect: function() { + return '#'; + }, + + toJSON: function() { + return Object.toJSON(this.toObject()); + }, + + clone: function() { + return new Hash(this); + } + } +})()); + +Hash.prototype.toTemplateReplacements = Hash.prototype.toObject; +Hash.from = $H; +var ObjectRange = Class.create(Enumerable, { + initialize: function(start, end, exclusive) { + this.start = start; + this.end = end; + this.exclusive = exclusive; + }, + + _each: function(iterator) { + var value = this.start; + while (this.include(value)) { + iterator(value); + value = value.succ(); + } + }, + + include: function(value) { + if (value < this.start) + return false; + if (this.exclusive) + return value < this.end; + return value <= this.end; + } +}); + +var $R = function(start, end, exclusive) { + return new ObjectRange(start, end, exclusive); +}; + +var Ajax = { + getTransport: function() { + return Try.these( + function() {return new XMLHttpRequest()}, + function() {return new ActiveXObject('Msxml2.XMLHTTP')}, + function() {return new ActiveXObject('Microsoft.XMLHTTP')} + ) || false; + }, + + activeRequestCount: 0 +}; + +Ajax.Responders = { + responders: [], + + _each: function(iterator) { + this.responders._each(iterator); + }, + + register: function(responder) { + if (!this.include(responder)) + this.responders.push(responder); + }, + + unregister: function(responder) { + this.responders = this.responders.without(responder); + }, + + dispatch: function(callback, request, transport, json) { + this.each(function(responder) { + if (Object.isFunction(responder[callback])) { + try { + responder[callback].apply(responder, [request, transport, json]); + } catch (e) { } + } + }); + } +}; + +Object.extend(Ajax.Responders, Enumerable); + +Ajax.Responders.register({ + onCreate: function() { Ajax.activeRequestCount++ }, + onComplete: function() { Ajax.activeRequestCount-- } +}); + +Ajax.Base = Class.create({ + initialize: function(options) { + this.options = { + method: 'post', + asynchronous: true, + contentType: 'application/x-www-form-urlencoded', + encoding: 'UTF-8', + parameters: '', + evalJSON: true, + evalJS: true + }; + Object.extend(this.options, options || { }); + + this.options.method = this.options.method.toLowerCase(); + + if (Object.isString(this.options.parameters)) + this.options.parameters = this.options.parameters.toQueryParams(); + else if (Object.isHash(this.options.parameters)) + this.options.parameters = this.options.parameters.toObject(); + } +}); + +Ajax.Request = Class.create(Ajax.Base, { + _complete: false, + + initialize: function($super, url, options) { + $super(options); + this.transport = Ajax.getTransport(); + this.request(url); + }, + + request: function(url) { + this.url = url; + this.method = this.options.method; + var params = Object.clone(this.options.parameters); + + if (!['get', 'post'].include(this.method)) { + // simulate other verbs over post + params['_method'] = this.method; + this.method = 'post'; + } + + this.parameters = params; + + if (params = Object.toQueryString(params)) { + // when GET, append parameters to URL + if (this.method == 'get') + this.url += (this.url.include('?') ? '&' : '?') + params; + else if (/Konqueror|Safari|KHTML/.test(navigator.userAgent)) + params += '&_='; + } + + try { + var response = new Ajax.Response(this); + if (this.options.onCreate) this.options.onCreate(response); + Ajax.Responders.dispatch('onCreate', this, response); + + this.transport.open(this.method.toUpperCase(), this.url, + this.options.asynchronous); + + if (this.options.asynchronous) this.respondToReadyState.bind(this).defer(1); + + this.transport.onreadystatechange = this.onStateChange.bind(this); + this.setRequestHeaders(); + + this.body = this.method == 'post' ? (this.options.postBody || params) : null; + this.transport.send(this.body); + + /* Force Firefox to handle ready state 4 for synchronous requests */ + if (!this.options.asynchronous && this.transport.overrideMimeType) + this.onStateChange(); + + } + catch (e) { + this.dispatchException(e); + } + }, + + onStateChange: function() { + var readyState = this.transport.readyState; + if (readyState > 1 && !((readyState == 4) && this._complete)) + this.respondToReadyState(this.transport.readyState); + }, + + setRequestHeaders: function() { + var headers = { + 'X-Requested-With': 'XMLHttpRequest', + 'X-Prototype-Version': Prototype.Version, + 'Accept': 'text/javascript, text/html, application/xml, text/xml, */*' + }; + + if (this.method == 'post') { + headers['Content-type'] = this.options.contentType + + (this.options.encoding ? '; charset=' + this.options.encoding : ''); + + /* Force "Connection: close" for older Mozilla browsers to work + * around a bug where XMLHttpRequest sends an incorrect + * Content-length header. See Mozilla Bugzilla #246651. + */ + if (this.transport.overrideMimeType && + (navigator.userAgent.match(/Gecko\/(\d{4})/) || [0,2005])[1] < 2005) + headers['Connection'] = 'close'; + } + + // user-defined headers + if (typeof this.options.requestHeaders == 'object') { + var extras = this.options.requestHeaders; + + if (Object.isFunction(extras.push)) + for (var i = 0, length = extras.length; i < length; i += 2) + headers[extras[i]] = extras[i+1]; + else + $H(extras).each(function(pair) { headers[pair.key] = pair.value }); + } + + for (var name in headers) + this.transport.setRequestHeader(name, headers[name]); + }, + + success: function() { + var status = this.getStatus(); + return !status || (status >= 200 && status < 300); + }, + + getStatus: function() { + try { + return this.transport.status || 0; + } catch (e) { return 0 } + }, + + respondToReadyState: function(readyState) { + var state = Ajax.Request.Events[readyState], response = new Ajax.Response(this); + + if (state == 'Complete') { + try { + this._complete = true; + (this.options['on' + response.status] + || this.options['on' + (this.success() ? 'Success' : 'Failure')] + || Prototype.emptyFunction)(response, response.headerJSON); + } catch (e) { + this.dispatchException(e); + } + + var contentType = response.getHeader('Content-type'); + if (this.options.evalJS == 'force' + || (this.options.evalJS && this.isSameOrigin() && contentType + && contentType.match(/^\s*(text|application)\/(x-)?(java|ecma)script(;.*)?\s*$/i))) + this.evalResponse(); + } + + try { + (this.options['on' + state] || Prototype.emptyFunction)(response, response.headerJSON); + Ajax.Responders.dispatch('on' + state, this, response, response.headerJSON); + } catch (e) { + this.dispatchException(e); + } + + if (state == 'Complete') { + // avoid memory leak in MSIE: clean up + this.transport.onreadystatechange = Prototype.emptyFunction; + } + }, + + isSameOrigin: function() { + var m = this.url.match(/^\s*https?:\/\/[^\/]*/); + return !m || (m[0] == '#{protocol}//#{domain}#{port}'.interpolate({ + protocol: location.protocol, + domain: document.domain, + port: location.port ? ':' + location.port : '' + })); + }, + + getHeader: function(name) { + try { + return this.transport.getResponseHeader(name) || null; + } catch (e) { return null } + }, + + evalResponse: function() { + try { + return eval((this.transport.responseText || '').unfilterJSON()); + } catch (e) { + this.dispatchException(e); + } + }, + + dispatchException: function(exception) { + (this.options.onException || Prototype.emptyFunction)(this, exception); + Ajax.Responders.dispatch('onException', this, exception); + } +}); + +Ajax.Request.Events = + ['Uninitialized', 'Loading', 'Loaded', 'Interactive', 'Complete']; + +Ajax.Response = Class.create({ + initialize: function(request){ + this.request = request; + var transport = this.transport = request.transport, + readyState = this.readyState = transport.readyState; + + if((readyState > 2 && !Prototype.Browser.IE) || readyState == 4) { + this.status = this.getStatus(); + this.statusText = this.getStatusText(); + this.responseText = String.interpret(transport.responseText); + this.headerJSON = this._getHeaderJSON(); + } + + if(readyState == 4) { + var xml = transport.responseXML; + this.responseXML = Object.isUndefined(xml) ? null : xml; + this.responseJSON = this._getResponseJSON(); + } + }, + + status: 0, + statusText: '', + + getStatus: Ajax.Request.prototype.getStatus, + + getStatusText: function() { + try { + return this.transport.statusText || ''; + } catch (e) { return '' } + }, + + getHeader: Ajax.Request.prototype.getHeader, + + getAllHeaders: function() { + try { + return this.getAllResponseHeaders(); + } catch (e) { return null } + }, + + getResponseHeader: function(name) { + return this.transport.getResponseHeader(name); + }, + + getAllResponseHeaders: function() { + return this.transport.getAllResponseHeaders(); + }, + + _getHeaderJSON: function() { + var json = this.getHeader('X-JSON'); + if (!json) return null; + json = decodeURIComponent(escape(json)); + try { + return json.evalJSON(this.request.options.sanitizeJSON || + !this.request.isSameOrigin()); + } catch (e) { + this.request.dispatchException(e); + } + }, + + _getResponseJSON: function() { + var options = this.request.options; + if (!options.evalJSON || (options.evalJSON != 'force' && + !(this.getHeader('Content-type') || '').include('application/json')) || + this.responseText.blank()) + return null; + try { + return this.responseText.evalJSON(options.sanitizeJSON || + !this.request.isSameOrigin()); + } catch (e) { + this.request.dispatchException(e); + } + } +}); + +Ajax.Updater = Class.create(Ajax.Request, { + initialize: function($super, container, url, options) { + this.container = { + success: (container.success || container), + failure: (container.failure || (container.success ? null : container)) + }; + + options = Object.clone(options); + var onComplete = options.onComplete; + options.onComplete = (function(response, json) { + this.updateContent(response.responseText); + if (Object.isFunction(onComplete)) onComplete(response, json); + }).bind(this); + + $super(url, options); + }, + + updateContent: function(responseText) { + var receiver = this.container[this.success() ? 'success' : 'failure'], + options = this.options; + + if (!options.evalScripts) responseText = responseText.stripScripts(); + + if (receiver = $(receiver)) { + if (options.insertion) { + if (Object.isString(options.insertion)) { + var insertion = { }; insertion[options.insertion] = responseText; + receiver.insert(insertion); + } + else options.insertion(receiver, responseText); + } + else receiver.update(responseText); + } + } +}); + +Ajax.PeriodicalUpdater = Class.create(Ajax.Base, { + initialize: function($super, container, url, options) { + $super(options); + this.onComplete = this.options.onComplete; + + this.frequency = (this.options.frequency || 2); + this.decay = (this.options.decay || 1); + + this.updater = { }; + this.container = container; + this.url = url; + + this.start(); + }, + + start: function() { + this.options.onComplete = this.updateComplete.bind(this); + this.onTimerEvent(); + }, + + stop: function() { + this.updater.options.onComplete = undefined; + clearTimeout(this.timer); + (this.onComplete || Prototype.emptyFunction).apply(this, arguments); + }, + + updateComplete: function(response) { + if (this.options.decay) { + this.decay = (response.responseText == this.lastText ? + this.decay * this.options.decay : 1); + + this.lastText = response.responseText; + } + this.timer = this.onTimerEvent.bind(this).delay(this.decay * this.frequency); + }, + + onTimerEvent: function() { + this.updater = new Ajax.Updater(this.container, this.url, this.options); + } +}); +function $(element) { + if (arguments.length > 1) { + for (var i = 0, elements = [], length = arguments.length; i < length; i++) + elements.push($(arguments[i])); + return elements; + } + if (Object.isString(element)) + element = document.getElementById(element); + return Element.extend(element); +} + +if (Prototype.BrowserFeatures.XPath) { + document._getElementsByXPath = function(expression, parentElement) { + var results = []; + var query = document.evaluate(expression, $(parentElement) || document, + null, XPathResult.ORDERED_NODE_SNAPSHOT_TYPE, null); + for (var i = 0, length = query.snapshotLength; i < length; i++) + results.push(Element.extend(query.snapshotItem(i))); + return results; + }; +} + +/*--------------------------------------------------------------------------*/ + +if (!window.Node) var Node = { }; + +if (!Node.ELEMENT_NODE) { + // DOM level 2 ECMAScript Language Binding + Object.extend(Node, { + ELEMENT_NODE: 1, + ATTRIBUTE_NODE: 2, + TEXT_NODE: 3, + CDATA_SECTION_NODE: 4, + ENTITY_REFERENCE_NODE: 5, + ENTITY_NODE: 6, + PROCESSING_INSTRUCTION_NODE: 7, + COMMENT_NODE: 8, + DOCUMENT_NODE: 9, + DOCUMENT_TYPE_NODE: 10, + DOCUMENT_FRAGMENT_NODE: 11, + NOTATION_NODE: 12 + }); +} + +(function() { + var element = this.Element; + this.Element = function(tagName, attributes) { + attributes = attributes || { }; + tagName = tagName.toLowerCase(); + var cache = Element.cache; + if (Prototype.Browser.IE && attributes.name) { + tagName = '<' + tagName + ' name="' + attributes.name + '">'; + delete attributes.name; + return Element.writeAttribute(document.createElement(tagName), attributes); + } + if (!cache[tagName]) cache[tagName] = Element.extend(document.createElement(tagName)); + return Element.writeAttribute(cache[tagName].cloneNode(false), attributes); + }; + Object.extend(this.Element, element || { }); + if (element) this.Element.prototype = element.prototype; +}).call(window); + +Element.cache = { }; + +Element.Methods = { + visible: function(element) { + return $(element).style.display != 'none'; + }, + + toggle: function(element) { + element = $(element); + Element[Element.visible(element) ? 'hide' : 'show'](element); + return element; + }, + + hide: function(element) { + element = $(element); + element.style.display = 'none'; + return element; + }, + + show: function(element) { + element = $(element); + element.style.display = ''; + return element; + }, + + remove: function(element) { + element = $(element); + element.parentNode.removeChild(element); + return element; + }, + + update: function(element, content) { + element = $(element); + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) return element.update().insert(content); + content = Object.toHTML(content); + element.innerHTML = content.stripScripts(); + content.evalScripts.bind(content).defer(); + return element; + }, + + replace: function(element, content) { + element = $(element); + if (content && content.toElement) content = content.toElement(); + else if (!Object.isElement(content)) { + content = Object.toHTML(content); + var range = element.ownerDocument.createRange(); + range.selectNode(element); + content.evalScripts.bind(content).defer(); + content = range.createContextualFragment(content.stripScripts()); + } + element.parentNode.replaceChild(content, element); + return element; + }, + + insert: function(element, insertions) { + element = $(element); + + if (Object.isString(insertions) || Object.isNumber(insertions) || + Object.isElement(insertions) || (insertions && (insertions.toElement || insertions.toHTML))) + insertions = {bottom:insertions}; + + var content, insert, tagName, childNodes; + + for (var position in insertions) { + content = insertions[position]; + position = position.toLowerCase(); + insert = Element._insertionTranslations[position]; + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) { + insert(element, content); + continue; + } + + content = Object.toHTML(content); + + tagName = ((position == 'before' || position == 'after') + ? element.parentNode : element).tagName.toUpperCase(); + + childNodes = Element._getContentFromAnonymousElement(tagName, content.stripScripts()); + + if (position == 'top' || position == 'after') childNodes.reverse(); + childNodes.each(insert.curry(element)); + + content.evalScripts.bind(content).defer(); + } + + return element; + }, + + wrap: function(element, wrapper, attributes) { + element = $(element); + if (Object.isElement(wrapper)) + $(wrapper).writeAttribute(attributes || { }); + else if (Object.isString(wrapper)) wrapper = new Element(wrapper, attributes); + else wrapper = new Element('div', wrapper); + if (element.parentNode) + element.parentNode.replaceChild(wrapper, element); + wrapper.appendChild(element); + return wrapper; + }, + + inspect: function(element) { + element = $(element); + var result = '<' + element.tagName.toLowerCase(); + $H({'id': 'id', 'className': 'class'}).each(function(pair) { + var property = pair.first(), attribute = pair.last(); + var value = (element[property] || '').toString(); + if (value) result += ' ' + attribute + '=' + value.inspect(true); + }); + return result + '>'; + }, + + recursivelyCollect: function(element, property) { + element = $(element); + var elements = []; + while (element = element[property]) + if (element.nodeType == 1) + elements.push(Element.extend(element)); + return elements; + }, + + ancestors: function(element) { + return $(element).recursivelyCollect('parentNode'); + }, + + descendants: function(element) { + return $(element).select("*"); + }, + + firstDescendant: function(element) { + element = $(element).firstChild; + while (element && element.nodeType != 1) element = element.nextSibling; + return $(element); + }, + + immediateDescendants: function(element) { + if (!(element = $(element).firstChild)) return []; + while (element && element.nodeType != 1) element = element.nextSibling; + if (element) return [element].concat($(element).nextSiblings()); + return []; + }, + + previousSiblings: function(element) { + return $(element).recursivelyCollect('previousSibling'); + }, + + nextSiblings: function(element) { + return $(element).recursivelyCollect('nextSibling'); + }, + + siblings: function(element) { + element = $(element); + return element.previousSiblings().reverse().concat(element.nextSiblings()); + }, + + match: function(element, selector) { + if (Object.isString(selector)) + selector = new Selector(selector); + return selector.match($(element)); + }, + + up: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(element.parentNode); + var ancestors = element.ancestors(); + return Object.isNumber(expression) ? ancestors[expression] : + Selector.findElement(ancestors, expression, index); + }, + + down: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return element.firstDescendant(); + return Object.isNumber(expression) ? element.descendants()[expression] : + Element.select(element, expression)[index || 0]; + }, + + previous: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(Selector.handlers.previousElementSibling(element)); + var previousSiblings = element.previousSiblings(); + return Object.isNumber(expression) ? previousSiblings[expression] : + Selector.findElement(previousSiblings, expression, index); + }, + + next: function(element, expression, index) { + element = $(element); + if (arguments.length == 1) return $(Selector.handlers.nextElementSibling(element)); + var nextSiblings = element.nextSiblings(); + return Object.isNumber(expression) ? nextSiblings[expression] : + Selector.findElement(nextSiblings, expression, index); + }, + + select: function() { + var args = $A(arguments), element = $(args.shift()); + return Selector.findChildElements(element, args); + }, + + adjacent: function() { + var args = $A(arguments), element = $(args.shift()); + return Selector.findChildElements(element.parentNode, args).without(element); + }, + + identify: function(element) { + element = $(element); + var id = element.readAttribute('id'), self = arguments.callee; + if (id) return id; + do { id = 'anonymous_element_' + self.counter++ } while ($(id)); + element.writeAttribute('id', id); + return id; + }, + + readAttribute: function(element, name) { + element = $(element); + if (Prototype.Browser.IE) { + var t = Element._attributeTranslations.read; + if (t.values[name]) return t.values[name](element, name); + if (t.names[name]) name = t.names[name]; + if (name.include(':')) { + return (!element.attributes || !element.attributes[name]) ? null : + element.attributes[name].value; + } + } + return element.getAttribute(name); + }, + + writeAttribute: function(element, name, value) { + element = $(element); + var attributes = { }, t = Element._attributeTranslations.write; + + if (typeof name == 'object') attributes = name; + else attributes[name] = Object.isUndefined(value) ? true : value; + + for (var attr in attributes) { + name = t.names[attr] || attr; + value = attributes[attr]; + if (t.values[attr]) name = t.values[attr](element, value); + if (value === false || value === null) + element.removeAttribute(name); + else if (value === true) + element.setAttribute(name, name); + else element.setAttribute(name, value); + } + return element; + }, + + getHeight: function(element) { + return $(element).getDimensions().height; + }, + + getWidth: function(element) { + return $(element).getDimensions().width; + }, + + classNames: function(element) { + return new Element.ClassNames(element); + }, + + hasClassName: function(element, className) { + if (!(element = $(element))) return; + var elementClassName = element.className; + return (elementClassName.length > 0 && (elementClassName == className || + new RegExp("(^|\\s)" + className + "(\\s|$)").test(elementClassName))); + }, + + addClassName: function(element, className) { + if (!(element = $(element))) return; + if (!element.hasClassName(className)) + element.className += (element.className ? ' ' : '') + className; + return element; + }, + + removeClassName: function(element, className) { + if (!(element = $(element))) return; + element.className = element.className.replace( + new RegExp("(^|\\s+)" + className + "(\\s+|$)"), ' ').strip(); + return element; + }, + + toggleClassName: function(element, className) { + if (!(element = $(element))) return; + return element[element.hasClassName(className) ? + 'removeClassName' : 'addClassName'](className); + }, + + // removes whitespace-only text node children + cleanWhitespace: function(element) { + element = $(element); + var node = element.firstChild; + while (node) { + var nextNode = node.nextSibling; + if (node.nodeType == 3 && !/\S/.test(node.nodeValue)) + element.removeChild(node); + node = nextNode; + } + return element; + }, + + empty: function(element) { + return $(element).innerHTML.blank(); + }, + + descendantOf: function(element, ancestor) { + element = $(element), ancestor = $(ancestor); + + if (element.compareDocumentPosition) + return (element.compareDocumentPosition(ancestor) & 8) === 8; + + if (ancestor.contains) + return ancestor.contains(element) && ancestor !== element; + + while (element = element.parentNode) + if (element == ancestor) return true; + + return false; + }, + + scrollTo: function(element) { + element = $(element); + var pos = element.cumulativeOffset(); + window.scrollTo(pos[0], pos[1]); + return element; + }, + + getStyle: function(element, style) { + element = $(element); + style = style == 'float' ? 'cssFloat' : style.camelize(); + var value = element.style[style]; + if (!value || value == 'auto') { + var css = document.defaultView.getComputedStyle(element, null); + value = css ? css[style] : null; + } + if (style == 'opacity') return value ? parseFloat(value) : 1.0; + return value == 'auto' ? null : value; + }, + + getOpacity: function(element) { + return $(element).getStyle('opacity'); + }, + + setStyle: function(element, styles) { + element = $(element); + var elementStyle = element.style, match; + if (Object.isString(styles)) { + element.style.cssText += ';' + styles; + return styles.include('opacity') ? + element.setOpacity(styles.match(/opacity:\s*(\d?\.?\d*)/)[1]) : element; + } + for (var property in styles) + if (property == 'opacity') element.setOpacity(styles[property]); + else + elementStyle[(property == 'float' || property == 'cssFloat') ? + (Object.isUndefined(elementStyle.styleFloat) ? 'cssFloat' : 'styleFloat') : + property] = styles[property]; + + return element; + }, + + setOpacity: function(element, value) { + element = $(element); + element.style.opacity = (value == 1 || value === '') ? '' : + (value < 0.00001) ? 0 : value; + return element; + }, + + getDimensions: function(element) { + element = $(element); + var display = element.getStyle('display'); + if (display != 'none' && display != null) // Safari bug + return {width: element.offsetWidth, height: element.offsetHeight}; + + // All *Width and *Height properties give 0 on elements with display none, + // so enable the element temporarily + var els = element.style; + var originalVisibility = els.visibility; + var originalPosition = els.position; + var originalDisplay = els.display; + els.visibility = 'hidden'; + els.position = 'absolute'; + els.display = 'block'; + var originalWidth = element.clientWidth; + var originalHeight = element.clientHeight; + els.display = originalDisplay; + els.position = originalPosition; + els.visibility = originalVisibility; + return {width: originalWidth, height: originalHeight}; + }, + + makePositioned: function(element) { + element = $(element); + var pos = Element.getStyle(element, 'position'); + if (pos == 'static' || !pos) { + element._madePositioned = true; + element.style.position = 'relative'; + // Opera returns the offset relative to the positioning context, when an + // element is position relative but top and left have not been defined + if (Prototype.Browser.Opera) { + element.style.top = 0; + element.style.left = 0; + } + } + return element; + }, + + undoPositioned: function(element) { + element = $(element); + if (element._madePositioned) { + element._madePositioned = undefined; + element.style.position = + element.style.top = + element.style.left = + element.style.bottom = + element.style.right = ''; + } + return element; + }, + + makeClipping: function(element) { + element = $(element); + if (element._overflow) return element; + element._overflow = Element.getStyle(element, 'overflow') || 'auto'; + if (element._overflow !== 'hidden') + element.style.overflow = 'hidden'; + return element; + }, + + undoClipping: function(element) { + element = $(element); + if (!element._overflow) return element; + element.style.overflow = element._overflow == 'auto' ? '' : element._overflow; + element._overflow = null; + return element; + }, + + cumulativeOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + element = element.offsetParent; + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + positionedOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + element = element.offsetParent; + if (element) { + if (element.tagName.toUpperCase() == 'BODY') break; + var p = Element.getStyle(element, 'position'); + if (p !== 'static') break; + } + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + absolutize: function(element) { + element = $(element); + if (element.getStyle('position') == 'absolute') return element; + // Position.prepare(); // To be done manually by Scripty when it needs it. + + var offsets = element.positionedOffset(); + var top = offsets[1]; + var left = offsets[0]; + var width = element.clientWidth; + var height = element.clientHeight; + + element._originalLeft = left - parseFloat(element.style.left || 0); + element._originalTop = top - parseFloat(element.style.top || 0); + element._originalWidth = element.style.width; + element._originalHeight = element.style.height; + + element.style.position = 'absolute'; + element.style.top = top + 'px'; + element.style.left = left + 'px'; + element.style.width = width + 'px'; + element.style.height = height + 'px'; + return element; + }, + + relativize: function(element) { + element = $(element); + if (element.getStyle('position') == 'relative') return element; + // Position.prepare(); // To be done manually by Scripty when it needs it. + + element.style.position = 'relative'; + var top = parseFloat(element.style.top || 0) - (element._originalTop || 0); + var left = parseFloat(element.style.left || 0) - (element._originalLeft || 0); + + element.style.top = top + 'px'; + element.style.left = left + 'px'; + element.style.height = element._originalHeight; + element.style.width = element._originalWidth; + return element; + }, + + cumulativeScrollOffset: function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.scrollTop || 0; + valueL += element.scrollLeft || 0; + element = element.parentNode; + } while (element); + return Element._returnOffset(valueL, valueT); + }, + + getOffsetParent: function(element) { + if (element.offsetParent) return $(element.offsetParent); + if (element == document.body) return $(element); + + while ((element = element.parentNode) && element != document.body) + if (Element.getStyle(element, 'position') != 'static') + return $(element); + + return $(document.body); + }, + + viewportOffset: function(forElement) { + var valueT = 0, valueL = 0; + + var element = forElement; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + + // Safari fix + if (element.offsetParent == document.body && + Element.getStyle(element, 'position') == 'absolute') break; + + } while (element = element.offsetParent); + + element = forElement; + do { + if (!Prototype.Browser.Opera || (element.tagName && (element.tagName.toUpperCase() == 'BODY'))) { + valueT -= element.scrollTop || 0; + valueL -= element.scrollLeft || 0; + } + } while (element = element.parentNode); + + return Element._returnOffset(valueL, valueT); + }, + + clonePosition: function(element, source) { + var options = Object.extend({ + setLeft: true, + setTop: true, + setWidth: true, + setHeight: true, + offsetTop: 0, + offsetLeft: 0 + }, arguments[2] || { }); + + // find page position of source + source = $(source); + var p = source.viewportOffset(); + + // find coordinate system to use + element = $(element); + var delta = [0, 0]; + var parent = null; + // delta [0,0] will do fine with position: fixed elements, + // position:absolute needs offsetParent deltas + if (Element.getStyle(element, 'position') == 'absolute') { + parent = element.getOffsetParent(); + delta = parent.viewportOffset(); + } + + // correct by body offsets (fixes Safari) + if (parent == document.body) { + delta[0] -= document.body.offsetLeft; + delta[1] -= document.body.offsetTop; + } + + // set position + if (options.setLeft) element.style.left = (p[0] - delta[0] + options.offsetLeft) + 'px'; + if (options.setTop) element.style.top = (p[1] - delta[1] + options.offsetTop) + 'px'; + if (options.setWidth) element.style.width = source.offsetWidth + 'px'; + if (options.setHeight) element.style.height = source.offsetHeight + 'px'; + return element; + } +}; + +Element.Methods.identify.counter = 1; + +Object.extend(Element.Methods, { + getElementsBySelector: Element.Methods.select, + childElements: Element.Methods.immediateDescendants +}); + +Element._attributeTranslations = { + write: { + names: { + className: 'class', + htmlFor: 'for' + }, + values: { } + } +}; + +if (Prototype.Browser.Opera) { + Element.Methods.getStyle = Element.Methods.getStyle.wrap( + function(proceed, element, style) { + switch (style) { + case 'left': case 'top': case 'right': case 'bottom': + if (proceed(element, 'position') === 'static') return null; + case 'height': case 'width': + // returns '0px' for hidden elements; we want it to return null + if (!Element.visible(element)) return null; + + // returns the border-box dimensions rather than the content-box + // dimensions, so we subtract padding and borders from the value + var dim = parseInt(proceed(element, style), 10); + + if (dim !== element['offset' + style.capitalize()]) + return dim + 'px'; + + var properties; + if (style === 'height') { + properties = ['border-top-width', 'padding-top', + 'padding-bottom', 'border-bottom-width']; + } + else { + properties = ['border-left-width', 'padding-left', + 'padding-right', 'border-right-width']; + } + return properties.inject(dim, function(memo, property) { + var val = proceed(element, property); + return val === null ? memo : memo - parseInt(val, 10); + }) + 'px'; + default: return proceed(element, style); + } + } + ); + + Element.Methods.readAttribute = Element.Methods.readAttribute.wrap( + function(proceed, element, attribute) { + if (attribute === 'title') return element.title; + return proceed(element, attribute); + } + ); +} + +else if (Prototype.Browser.IE) { + // IE doesn't report offsets correctly for static elements, so we change them + // to "relative" to get the values, then change them back. + Element.Methods.getOffsetParent = Element.Methods.getOffsetParent.wrap( + function(proceed, element) { + element = $(element); + // IE throws an error if element is not in document + try { element.offsetParent } + catch(e) { return $(document.body) } + var position = element.getStyle('position'); + if (position !== 'static') return proceed(element); + element.setStyle({ position: 'relative' }); + var value = proceed(element); + element.setStyle({ position: position }); + return value; + } + ); + + $w('positionedOffset viewportOffset').each(function(method) { + Element.Methods[method] = Element.Methods[method].wrap( + function(proceed, element) { + element = $(element); + try { element.offsetParent } + catch(e) { return Element._returnOffset(0,0) } + var position = element.getStyle('position'); + if (position !== 'static') return proceed(element); + // Trigger hasLayout on the offset parent so that IE6 reports + // accurate offsetTop and offsetLeft values for position: fixed. + var offsetParent = element.getOffsetParent(); + if (offsetParent && offsetParent.getStyle('position') === 'fixed') + offsetParent.setStyle({ zoom: 1 }); + element.setStyle({ position: 'relative' }); + var value = proceed(element); + element.setStyle({ position: position }); + return value; + } + ); + }); + + Element.Methods.cumulativeOffset = Element.Methods.cumulativeOffset.wrap( + function(proceed, element) { + try { element.offsetParent } + catch(e) { return Element._returnOffset(0,0) } + return proceed(element); + } + ); + + Element.Methods.getStyle = function(element, style) { + element = $(element); + style = (style == 'float' || style == 'cssFloat') ? 'styleFloat' : style.camelize(); + var value = element.style[style]; + if (!value && element.currentStyle) value = element.currentStyle[style]; + + if (style == 'opacity') { + if (value = (element.getStyle('filter') || '').match(/alpha\(opacity=(.*)\)/)) + if (value[1]) return parseFloat(value[1]) / 100; + return 1.0; + } + + if (value == 'auto') { + if ((style == 'width' || style == 'height') && (element.getStyle('display') != 'none')) + return element['offset' + style.capitalize()] + 'px'; + return null; + } + return value; + }; + + Element.Methods.setOpacity = function(element, value) { + function stripAlpha(filter){ + return filter.replace(/alpha\([^\)]*\)/gi,''); + } + element = $(element); + var currentStyle = element.currentStyle; + if ((currentStyle && !currentStyle.hasLayout) || + (!currentStyle && element.style.zoom == 'normal')) + element.style.zoom = 1; + + var filter = element.getStyle('filter'), style = element.style; + if (value == 1 || value === '') { + (filter = stripAlpha(filter)) ? + style.filter = filter : style.removeAttribute('filter'); + return element; + } else if (value < 0.00001) value = 0; + style.filter = stripAlpha(filter) + + 'alpha(opacity=' + (value * 100) + ')'; + return element; + }; + + Element._attributeTranslations = { + read: { + names: { + 'class': 'className', + 'for': 'htmlFor' + }, + values: { + _getAttr: function(element, attribute) { + return element.getAttribute(attribute, 2); + }, + _getAttrNode: function(element, attribute) { + var node = element.getAttributeNode(attribute); + return node ? node.value : ""; + }, + _getEv: function(element, attribute) { + attribute = element.getAttribute(attribute); + return attribute ? attribute.toString().slice(23, -2) : null; + }, + _flag: function(element, attribute) { + return $(element).hasAttribute(attribute) ? attribute : null; + }, + style: function(element) { + return element.style.cssText.toLowerCase(); + }, + title: function(element) { + return element.title; + } + } + } + }; + + Element._attributeTranslations.write = { + names: Object.extend({ + cellpadding: 'cellPadding', + cellspacing: 'cellSpacing' + }, Element._attributeTranslations.read.names), + values: { + checked: function(element, value) { + element.checked = !!value; + }, + + style: function(element, value) { + element.style.cssText = value ? value : ''; + } + } + }; + + Element._attributeTranslations.has = {}; + + $w('colSpan rowSpan vAlign dateTime accessKey tabIndex ' + + 'encType maxLength readOnly longDesc frameBorder').each(function(attr) { + Element._attributeTranslations.write.names[attr.toLowerCase()] = attr; + Element._attributeTranslations.has[attr.toLowerCase()] = attr; + }); + + (function(v) { + Object.extend(v, { + href: v._getAttr, + src: v._getAttr, + type: v._getAttr, + action: v._getAttrNode, + disabled: v._flag, + checked: v._flag, + readonly: v._flag, + multiple: v._flag, + onload: v._getEv, + onunload: v._getEv, + onclick: v._getEv, + ondblclick: v._getEv, + onmousedown: v._getEv, + onmouseup: v._getEv, + onmouseover: v._getEv, + onmousemove: v._getEv, + onmouseout: v._getEv, + onfocus: v._getEv, + onblur: v._getEv, + onkeypress: v._getEv, + onkeydown: v._getEv, + onkeyup: v._getEv, + onsubmit: v._getEv, + onreset: v._getEv, + onselect: v._getEv, + onchange: v._getEv + }); + })(Element._attributeTranslations.read.values); +} + +else if (Prototype.Browser.Gecko && /rv:1\.8\.0/.test(navigator.userAgent)) { + Element.Methods.setOpacity = function(element, value) { + element = $(element); + element.style.opacity = (value == 1) ? 0.999999 : + (value === '') ? '' : (value < 0.00001) ? 0 : value; + return element; + }; +} + +else if (Prototype.Browser.WebKit) { + Element.Methods.setOpacity = function(element, value) { + element = $(element); + element.style.opacity = (value == 1 || value === '') ? '' : + (value < 0.00001) ? 0 : value; + + if (value == 1) + if(element.tagName.toUpperCase() == 'IMG' && element.width) { + element.width++; element.width--; + } else try { + var n = document.createTextNode(' '); + element.appendChild(n); + element.removeChild(n); + } catch (e) { } + + return element; + }; + + // Safari returns margins on body which is incorrect if the child is absolutely + // positioned. For performance reasons, redefine Element#cumulativeOffset for + // KHTML/WebKit only. + Element.Methods.cumulativeOffset = function(element) { + var valueT = 0, valueL = 0; + do { + valueT += element.offsetTop || 0; + valueL += element.offsetLeft || 0; + if (element.offsetParent == document.body) + if (Element.getStyle(element, 'position') == 'absolute') break; + + element = element.offsetParent; + } while (element); + + return Element._returnOffset(valueL, valueT); + }; +} + +if (Prototype.Browser.IE || Prototype.Browser.Opera) { + // IE and Opera are missing .innerHTML support for TABLE-related and SELECT elements + Element.Methods.update = function(element, content) { + element = $(element); + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) return element.update().insert(content); + + content = Object.toHTML(content); + var tagName = element.tagName.toUpperCase(); + + if (tagName in Element._insertionTranslations.tags) { + $A(element.childNodes).each(function(node) { element.removeChild(node) }); + Element._getContentFromAnonymousElement(tagName, content.stripScripts()) + .each(function(node) { element.appendChild(node) }); + } + else element.innerHTML = content.stripScripts(); + + content.evalScripts.bind(content).defer(); + return element; + }; +} + +if ('outerHTML' in document.createElement('div')) { + Element.Methods.replace = function(element, content) { + element = $(element); + + if (content && content.toElement) content = content.toElement(); + if (Object.isElement(content)) { + element.parentNode.replaceChild(content, element); + return element; + } + + content = Object.toHTML(content); + var parent = element.parentNode, tagName = parent.tagName.toUpperCase(); + + if (Element._insertionTranslations.tags[tagName]) { + var nextSibling = element.next(); + var fragments = Element._getContentFromAnonymousElement(tagName, content.stripScripts()); + parent.removeChild(element); + if (nextSibling) + fragments.each(function(node) { parent.insertBefore(node, nextSibling) }); + else + fragments.each(function(node) { parent.appendChild(node) }); + } + else element.outerHTML = content.stripScripts(); + + content.evalScripts.bind(content).defer(); + return element; + }; +} + +Element._returnOffset = function(l, t) { + var result = [l, t]; + result.left = l; + result.top = t; + return result; +}; + +Element._getContentFromAnonymousElement = function(tagName, html) { + var div = new Element('div'), t = Element._insertionTranslations.tags[tagName]; + if (t) { + div.innerHTML = t[0] + html + t[1]; + t[2].times(function() { div = div.firstChild }); + } else div.innerHTML = html; + return $A(div.childNodes); +}; + +Element._insertionTranslations = { + before: function(element, node) { + element.parentNode.insertBefore(node, element); + }, + top: function(element, node) { + element.insertBefore(node, element.firstChild); + }, + bottom: function(element, node) { + element.appendChild(node); + }, + after: function(element, node) { + element.parentNode.insertBefore(node, element.nextSibling); + }, + tags: { + TABLE: ['', '
    ', 1], + TBODY: ['', '
    ', 2], + TR: ['', '
    ', 3], + TD: ['
    ', '
    ', 4], + SELECT: ['', 1] + } +}; + +(function() { + Object.extend(this.tags, { + THEAD: this.tags.TBODY, + TFOOT: this.tags.TBODY, + TH: this.tags.TD + }); +}).call(Element._insertionTranslations); + +Element.Methods.Simulated = { + hasAttribute: function(element, attribute) { + attribute = Element._attributeTranslations.has[attribute] || attribute; + var node = $(element).getAttributeNode(attribute); + return !!(node && node.specified); + } +}; + +Element.Methods.ByTag = { }; + +Object.extend(Element, Element.Methods); + +if (!Prototype.BrowserFeatures.ElementExtensions && + document.createElement('div')['__proto__']) { + window.HTMLElement = { }; + window.HTMLElement.prototype = document.createElement('div')['__proto__']; + Prototype.BrowserFeatures.ElementExtensions = true; +} + +Element.extend = (function() { + if (Prototype.BrowserFeatures.SpecificElementExtensions) + return Prototype.K; + + var Methods = { }, ByTag = Element.Methods.ByTag; + + var extend = Object.extend(function(element) { + if (!element || element._extendedByPrototype || + element.nodeType != 1 || element == window) return element; + + var methods = Object.clone(Methods), + tagName = element.tagName.toUpperCase(), property, value; + + // extend methods for specific tags + if (ByTag[tagName]) Object.extend(methods, ByTag[tagName]); + + for (property in methods) { + value = methods[property]; + if (Object.isFunction(value) && !(property in element)) + element[property] = value.methodize(); + } + + element._extendedByPrototype = Prototype.emptyFunction; + return element; + + }, { + refresh: function() { + // extend methods for all tags (Safari doesn't need this) + if (!Prototype.BrowserFeatures.ElementExtensions) { + Object.extend(Methods, Element.Methods); + Object.extend(Methods, Element.Methods.Simulated); + } + } + }); + + extend.refresh(); + return extend; +})(); + +Element.hasAttribute = function(element, attribute) { + if (element.hasAttribute) return element.hasAttribute(attribute); + return Element.Methods.Simulated.hasAttribute(element, attribute); +}; + +Element.addMethods = function(methods) { + var F = Prototype.BrowserFeatures, T = Element.Methods.ByTag; + + if (!methods) { + Object.extend(Form, Form.Methods); + Object.extend(Form.Element, Form.Element.Methods); + Object.extend(Element.Methods.ByTag, { + "FORM": Object.clone(Form.Methods), + "INPUT": Object.clone(Form.Element.Methods), + "SELECT": Object.clone(Form.Element.Methods), + "TEXTAREA": Object.clone(Form.Element.Methods) + }); + } + + if (arguments.length == 2) { + var tagName = methods; + methods = arguments[1]; + } + + if (!tagName) Object.extend(Element.Methods, methods || { }); + else { + if (Object.isArray(tagName)) tagName.each(extend); + else extend(tagName); + } + + function extend(tagName) { + tagName = tagName.toUpperCase(); + if (!Element.Methods.ByTag[tagName]) + Element.Methods.ByTag[tagName] = { }; + Object.extend(Element.Methods.ByTag[tagName], methods); + } + + function copy(methods, destination, onlyIfAbsent) { + onlyIfAbsent = onlyIfAbsent || false; + for (var property in methods) { + var value = methods[property]; + if (!Object.isFunction(value)) continue; + if (!onlyIfAbsent || !(property in destination)) + destination[property] = value.methodize(); + } + } + + function findDOMClass(tagName) { + var klass; + var trans = { + "OPTGROUP": "OptGroup", "TEXTAREA": "TextArea", "P": "Paragraph", + "FIELDSET": "FieldSet", "UL": "UList", "OL": "OList", "DL": "DList", + "DIR": "Directory", "H1": "Heading", "H2": "Heading", "H3": "Heading", + "H4": "Heading", "H5": "Heading", "H6": "Heading", "Q": "Quote", + "INS": "Mod", "DEL": "Mod", "A": "Anchor", "IMG": "Image", "CAPTION": + "TableCaption", "COL": "TableCol", "COLGROUP": "TableCol", "THEAD": + "TableSection", "TFOOT": "TableSection", "TBODY": "TableSection", "TR": + "TableRow", "TH": "TableCell", "TD": "TableCell", "FRAMESET": + "FrameSet", "IFRAME": "IFrame" + }; + if (trans[tagName]) klass = 'HTML' + trans[tagName] + 'Element'; + if (window[klass]) return window[klass]; + klass = 'HTML' + tagName + 'Element'; + if (window[klass]) return window[klass]; + klass = 'HTML' + tagName.capitalize() + 'Element'; + if (window[klass]) return window[klass]; + + window[klass] = { }; + window[klass].prototype = document.createElement(tagName)['__proto__']; + return window[klass]; + } + + if (F.ElementExtensions) { + copy(Element.Methods, HTMLElement.prototype); + copy(Element.Methods.Simulated, HTMLElement.prototype, true); + } + + if (F.SpecificElementExtensions) { + for (var tag in Element.Methods.ByTag) { + var klass = findDOMClass(tag); + if (Object.isUndefined(klass)) continue; + copy(T[tag], klass.prototype); + } + } + + Object.extend(Element, Element.Methods); + delete Element.ByTag; + + if (Element.extend.refresh) Element.extend.refresh(); + Element.cache = { }; +}; + +document.viewport = { + getDimensions: function() { + var dimensions = { }, B = Prototype.Browser; + $w('width height').each(function(d) { + var D = d.capitalize(); + if (B.WebKit && !document.evaluate) { + // Safari <3.0 needs self.innerWidth/Height + dimensions[d] = self['inner' + D]; + } else if (B.Opera && parseFloat(window.opera.version()) < 9.5) { + // Opera <9.5 needs document.body.clientWidth/Height + dimensions[d] = document.body['client' + D] + } else { + dimensions[d] = document.documentElement['client' + D]; + } + }); + return dimensions; + }, + + getWidth: function() { + return this.getDimensions().width; + }, + + getHeight: function() { + return this.getDimensions().height; + }, + + getScrollOffsets: function() { + return Element._returnOffset( + window.pageXOffset || document.documentElement.scrollLeft || document.body.scrollLeft, + window.pageYOffset || document.documentElement.scrollTop || document.body.scrollTop); + } +}; +/* Portions of the Selector class are derived from Jack Slocum's DomQuery, + * part of YUI-Ext version 0.40, distributed under the terms of an MIT-style + * license. Please see http://www.yui-ext.com/ for more information. */ + +var Selector = Class.create({ + initialize: function(expression) { + this.expression = expression.strip(); + + if (this.shouldUseSelectorsAPI()) { + this.mode = 'selectorsAPI'; + } else if (this.shouldUseXPath()) { + this.mode = 'xpath'; + this.compileXPathMatcher(); + } else { + this.mode = "normal"; + this.compileMatcher(); + } + + }, + + shouldUseXPath: function() { + if (!Prototype.BrowserFeatures.XPath) return false; + + var e = this.expression; + + // Safari 3 chokes on :*-of-type and :empty + if (Prototype.Browser.WebKit && + (e.include("-of-type") || e.include(":empty"))) + return false; + + // XPath can't do namespaced attributes, nor can it read + // the "checked" property from DOM nodes + if ((/(\[[\w-]*?:|:checked)/).test(e)) + return false; + + return true; + }, + + shouldUseSelectorsAPI: function() { + if (!Prototype.BrowserFeatures.SelectorsAPI) return false; + + if (!Selector._div) Selector._div = new Element('div'); + + // Make sure the browser treats the selector as valid. Test on an + // isolated element to minimize cost of this check. + try { + Selector._div.querySelector(this.expression); + } catch(e) { + return false; + } + + return true; + }, + + compileMatcher: function() { + var e = this.expression, ps = Selector.patterns, h = Selector.handlers, + c = Selector.criteria, le, p, m; + + if (Selector._cache[e]) { + this.matcher = Selector._cache[e]; + return; + } + + this.matcher = ["this.matcher = function(root) {", + "var r = root, h = Selector.handlers, c = false, n;"]; + + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + p = ps[i]; + if (m = e.match(p)) { + this.matcher.push(Object.isFunction(c[i]) ? c[i](m) : + new Template(c[i]).evaluate(m)); + e = e.replace(m[0], ''); + break; + } + } + } + + this.matcher.push("return h.unique(n);\n}"); + eval(this.matcher.join('\n')); + Selector._cache[this.expression] = this.matcher; + }, + + compileXPathMatcher: function() { + var e = this.expression, ps = Selector.patterns, + x = Selector.xpath, le, m; + + if (Selector._cache[e]) { + this.xpath = Selector._cache[e]; return; + } + + this.matcher = ['.//*']; + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + if (m = e.match(ps[i])) { + this.matcher.push(Object.isFunction(x[i]) ? x[i](m) : + new Template(x[i]).evaluate(m)); + e = e.replace(m[0], ''); + break; + } + } + } + + this.xpath = this.matcher.join(''); + Selector._cache[this.expression] = this.xpath; + }, + + findElements: function(root) { + root = root || document; + var e = this.expression, results; + + switch (this.mode) { + case 'selectorsAPI': + // querySelectorAll queries document-wide, then filters to descendants + // of the context element. That's not what we want. + // Add an explicit context to the selector if necessary. + if (root !== document) { + var oldId = root.id, id = $(root).identify(); + e = "#" + id + " " + e; + } + + results = $A(root.querySelectorAll(e)).map(Element.extend); + root.id = oldId; + + return results; + case 'xpath': + return document._getElementsByXPath(this.xpath, root); + default: + return this.matcher(root); + } + }, + + match: function(element) { + this.tokens = []; + + var e = this.expression, ps = Selector.patterns, as = Selector.assertions; + var le, p, m; + + while (e && le !== e && (/\S/).test(e)) { + le = e; + for (var i in ps) { + p = ps[i]; + if (m = e.match(p)) { + // use the Selector.assertions methods unless the selector + // is too complex. + if (as[i]) { + this.tokens.push([i, Object.clone(m)]); + e = e.replace(m[0], ''); + } else { + // reluctantly do a document-wide search + // and look for a match in the array + return this.findElements(document).include(element); + } + } + } + } + + var match = true, name, matches; + for (var i = 0, token; token = this.tokens[i]; i++) { + name = token[0], matches = token[1]; + if (!Selector.assertions[name](element, matches)) { + match = false; break; + } + } + + return match; + }, + + toString: function() { + return this.expression; + }, + + inspect: function() { + return "#"; + } +}); + +Object.extend(Selector, { + _cache: { }, + + xpath: { + descendant: "//*", + child: "/*", + adjacent: "/following-sibling::*[1]", + laterSibling: '/following-sibling::*', + tagName: function(m) { + if (m[1] == '*') return ''; + return "[local-name()='" + m[1].toLowerCase() + + "' or local-name()='" + m[1].toUpperCase() + "']"; + }, + className: "[contains(concat(' ', @class, ' '), ' #{1} ')]", + id: "[@id='#{1}']", + attrPresence: function(m) { + m[1] = m[1].toLowerCase(); + return new Template("[@#{1}]").evaluate(m); + }, + attr: function(m) { + m[1] = m[1].toLowerCase(); + m[3] = m[5] || m[6]; + return new Template(Selector.xpath.operators[m[2]]).evaluate(m); + }, + pseudo: function(m) { + var h = Selector.xpath.pseudos[m[1]]; + if (!h) return ''; + if (Object.isFunction(h)) return h(m); + return new Template(Selector.xpath.pseudos[m[1]]).evaluate(m); + }, + operators: { + '=': "[@#{1}='#{3}']", + '!=': "[@#{1}!='#{3}']", + '^=': "[starts-with(@#{1}, '#{3}')]", + '$=': "[substring(@#{1}, (string-length(@#{1}) - string-length('#{3}') + 1))='#{3}']", + '*=': "[contains(@#{1}, '#{3}')]", + '~=': "[contains(concat(' ', @#{1}, ' '), ' #{3} ')]", + '|=': "[contains(concat('-', @#{1}, '-'), '-#{3}-')]" + }, + pseudos: { + 'first-child': '[not(preceding-sibling::*)]', + 'last-child': '[not(following-sibling::*)]', + 'only-child': '[not(preceding-sibling::* or following-sibling::*)]', + 'empty': "[count(*) = 0 and (count(text()) = 0)]", + 'checked': "[@checked]", + 'disabled': "[(@disabled) and (@type!='hidden')]", + 'enabled': "[not(@disabled) and (@type!='hidden')]", + 'not': function(m) { + var e = m[6], p = Selector.patterns, + x = Selector.xpath, le, v; + + var exclusion = []; + while (e && le != e && (/\S/).test(e)) { + le = e; + for (var i in p) { + if (m = e.match(p[i])) { + v = Object.isFunction(x[i]) ? x[i](m) : new Template(x[i]).evaluate(m); + exclusion.push("(" + v.substring(1, v.length - 1) + ")"); + e = e.replace(m[0], ''); + break; + } + } + } + return "[not(" + exclusion.join(" and ") + ")]"; + }, + 'nth-child': function(m) { + return Selector.xpath.pseudos.nth("(count(./preceding-sibling::*) + 1) ", m); + }, + 'nth-last-child': function(m) { + return Selector.xpath.pseudos.nth("(count(./following-sibling::*) + 1) ", m); + }, + 'nth-of-type': function(m) { + return Selector.xpath.pseudos.nth("position() ", m); + }, + 'nth-last-of-type': function(m) { + return Selector.xpath.pseudos.nth("(last() + 1 - position()) ", m); + }, + 'first-of-type': function(m) { + m[6] = "1"; return Selector.xpath.pseudos['nth-of-type'](m); + }, + 'last-of-type': function(m) { + m[6] = "1"; return Selector.xpath.pseudos['nth-last-of-type'](m); + }, + 'only-of-type': function(m) { + var p = Selector.xpath.pseudos; return p['first-of-type'](m) + p['last-of-type'](m); + }, + nth: function(fragment, m) { + var mm, formula = m[6], predicate; + if (formula == 'even') formula = '2n+0'; + if (formula == 'odd') formula = '2n+1'; + if (mm = formula.match(/^(\d+)$/)) // digit only + return '[' + fragment + "= " + mm[1] + ']'; + if (mm = formula.match(/^(-?\d*)?n(([+-])(\d+))?/)) { // an+b + if (mm[1] == "-") mm[1] = -1; + var a = mm[1] ? Number(mm[1]) : 1; + var b = mm[2] ? Number(mm[2]) : 0; + predicate = "[((#{fragment} - #{b}) mod #{a} = 0) and " + + "((#{fragment} - #{b}) div #{a} >= 0)]"; + return new Template(predicate).evaluate({ + fragment: fragment, a: a, b: b }); + } + } + } + }, + + criteria: { + tagName: 'n = h.tagName(n, r, "#{1}", c); c = false;', + className: 'n = h.className(n, r, "#{1}", c); c = false;', + id: 'n = h.id(n, r, "#{1}", c); c = false;', + attrPresence: 'n = h.attrPresence(n, r, "#{1}", c); c = false;', + attr: function(m) { + m[3] = (m[5] || m[6]); + return new Template('n = h.attr(n, r, "#{1}", "#{3}", "#{2}", c); c = false;').evaluate(m); + }, + pseudo: function(m) { + if (m[6]) m[6] = m[6].replace(/"/g, '\\"'); + return new Template('n = h.pseudo(n, "#{1}", "#{6}", r, c); c = false;').evaluate(m); + }, + descendant: 'c = "descendant";', + child: 'c = "child";', + adjacent: 'c = "adjacent";', + laterSibling: 'c = "laterSibling";' + }, + + patterns: { + // combinators must be listed first + // (and descendant needs to be last combinator) + laterSibling: /^\s*~\s*/, + child: /^\s*>\s*/, + adjacent: /^\s*\+\s*/, + descendant: /^\s/, + + // selectors follow + tagName: /^\s*(\*|[\w\-]+)(\b|$)?/, + id: /^#([\w\-\*]+)(\b|$)/, + className: /^\.([\w\-\*]+)(\b|$)/, + pseudo: +/^:((first|last|nth|nth-last|only)(-child|-of-type)|empty|checked|(en|dis)abled|not)(\((.*?)\))?(\b|$|(?=\s|[:+~>]))/, + attrPresence: /^\[((?:[\w]+:)?[\w]+)\]/, + attr: /\[((?:[\w-]*:)?[\w-]+)\s*(?:([!^$*~|]?=)\s*((['"])([^\4]*?)\4|([^'"][^\]]*?)))?\]/ + }, + + // for Selector.match and Element#match + assertions: { + tagName: function(element, matches) { + return matches[1].toUpperCase() == element.tagName.toUpperCase(); + }, + + className: function(element, matches) { + return Element.hasClassName(element, matches[1]); + }, + + id: function(element, matches) { + return element.id === matches[1]; + }, + + attrPresence: function(element, matches) { + return Element.hasAttribute(element, matches[1]); + }, + + attr: function(element, matches) { + var nodeValue = Element.readAttribute(element, matches[1]); + return nodeValue && Selector.operators[matches[2]](nodeValue, matches[5] || matches[6]); + } + }, + + handlers: { + // UTILITY FUNCTIONS + // joins two collections + concat: function(a, b) { + for (var i = 0, node; node = b[i]; i++) + a.push(node); + return a; + }, + + // marks an array of nodes for counting + mark: function(nodes) { + var _true = Prototype.emptyFunction; + for (var i = 0, node; node = nodes[i]; i++) + node._countedByPrototype = _true; + return nodes; + }, + + unmark: function(nodes) { + for (var i = 0, node; node = nodes[i]; i++) + node._countedByPrototype = undefined; + return nodes; + }, + + // mark each child node with its position (for nth calls) + // "ofType" flag indicates whether we're indexing for nth-of-type + // rather than nth-child + index: function(parentNode, reverse, ofType) { + parentNode._countedByPrototype = Prototype.emptyFunction; + if (reverse) { + for (var nodes = parentNode.childNodes, i = nodes.length - 1, j = 1; i >= 0; i--) { + var node = nodes[i]; + if (node.nodeType == 1 && (!ofType || node._countedByPrototype)) node.nodeIndex = j++; + } + } else { + for (var i = 0, j = 1, nodes = parentNode.childNodes; node = nodes[i]; i++) + if (node.nodeType == 1 && (!ofType || node._countedByPrototype)) node.nodeIndex = j++; + } + }, + + // filters out duplicates and extends all nodes + unique: function(nodes) { + if (nodes.length == 0) return nodes; + var results = [], n; + for (var i = 0, l = nodes.length; i < l; i++) + if (!(n = nodes[i])._countedByPrototype) { + n._countedByPrototype = Prototype.emptyFunction; + results.push(Element.extend(n)); + } + return Selector.handlers.unmark(results); + }, + + // COMBINATOR FUNCTIONS + descendant: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + h.concat(results, node.getElementsByTagName('*')); + return results; + }, + + child: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) { + for (var j = 0, child; child = node.childNodes[j]; j++) + if (child.nodeType == 1 && child.tagName != '!') results.push(child); + } + return results; + }, + + adjacent: function(nodes) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + var next = this.nextElementSibling(node); + if (next) results.push(next); + } + return results; + }, + + laterSibling: function(nodes) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + h.concat(results, Element.nextSiblings(node)); + return results; + }, + + nextElementSibling: function(node) { + while (node = node.nextSibling) + if (node.nodeType == 1) return node; + return null; + }, + + previousElementSibling: function(node) { + while (node = node.previousSibling) + if (node.nodeType == 1) return node; + return null; + }, + + // TOKEN FUNCTIONS + tagName: function(nodes, root, tagName, combinator) { + var uTagName = tagName.toUpperCase(); + var results = [], h = Selector.handlers; + if (nodes) { + if (combinator) { + // fastlane for ordinary descendant combinators + if (combinator == "descendant") { + for (var i = 0, node; node = nodes[i]; i++) + h.concat(results, node.getElementsByTagName(tagName)); + return results; + } else nodes = this[combinator](nodes); + if (tagName == "*") return nodes; + } + for (var i = 0, node; node = nodes[i]; i++) + if (node.tagName.toUpperCase() === uTagName) results.push(node); + return results; + } else return root.getElementsByTagName(tagName); + }, + + id: function(nodes, root, id, combinator) { + var targetNode = $(id), h = Selector.handlers; + if (!targetNode) return []; + if (!nodes && root == document) return [targetNode]; + if (nodes) { + if (combinator) { + if (combinator == 'child') { + for (var i = 0, node; node = nodes[i]; i++) + if (targetNode.parentNode == node) return [targetNode]; + } else if (combinator == 'descendant') { + for (var i = 0, node; node = nodes[i]; i++) + if (Element.descendantOf(targetNode, node)) return [targetNode]; + } else if (combinator == 'adjacent') { + for (var i = 0, node; node = nodes[i]; i++) + if (Selector.handlers.previousElementSibling(targetNode) == node) + return [targetNode]; + } else nodes = h[combinator](nodes); + } + for (var i = 0, node; node = nodes[i]; i++) + if (node == targetNode) return [targetNode]; + return []; + } + return (targetNode && Element.descendantOf(targetNode, root)) ? [targetNode] : []; + }, + + className: function(nodes, root, className, combinator) { + if (nodes && combinator) nodes = this[combinator](nodes); + return Selector.handlers.byClassName(nodes, root, className); + }, + + byClassName: function(nodes, root, className) { + if (!nodes) nodes = Selector.handlers.descendant([root]); + var needle = ' ' + className + ' '; + for (var i = 0, results = [], node, nodeClassName; node = nodes[i]; i++) { + nodeClassName = node.className; + if (nodeClassName.length == 0) continue; + if (nodeClassName == className || (' ' + nodeClassName + ' ').include(needle)) + results.push(node); + } + return results; + }, + + attrPresence: function(nodes, root, attr, combinator) { + if (!nodes) nodes = root.getElementsByTagName("*"); + if (nodes && combinator) nodes = this[combinator](nodes); + var results = []; + for (var i = 0, node; node = nodes[i]; i++) + if (Element.hasAttribute(node, attr)) results.push(node); + return results; + }, + + attr: function(nodes, root, attr, value, operator, combinator) { + if (!nodes) nodes = root.getElementsByTagName("*"); + if (nodes && combinator) nodes = this[combinator](nodes); + var handler = Selector.operators[operator], results = []; + for (var i = 0, node; node = nodes[i]; i++) { + var nodeValue = Element.readAttribute(node, attr); + if (nodeValue === null) continue; + if (handler(nodeValue, value)) results.push(node); + } + return results; + }, + + pseudo: function(nodes, name, value, root, combinator) { + if (nodes && combinator) nodes = this[combinator](nodes); + if (!nodes) nodes = root.getElementsByTagName("*"); + return Selector.pseudos[name](nodes, value, root); + } + }, + + pseudos: { + 'first-child': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + if (Selector.handlers.previousElementSibling(node)) continue; + results.push(node); + } + return results; + }, + 'last-child': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + if (Selector.handlers.nextElementSibling(node)) continue; + results.push(node); + } + return results; + }, + 'only-child': function(nodes, value, root) { + var h = Selector.handlers; + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!h.previousElementSibling(node) && !h.nextElementSibling(node)) + results.push(node); + return results; + }, + 'nth-child': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root); + }, + 'nth-last-child': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, true); + }, + 'nth-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, false, true); + }, + 'nth-last-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, formula, root, true, true); + }, + 'first-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, "1", root, false, true); + }, + 'last-of-type': function(nodes, formula, root) { + return Selector.pseudos.nth(nodes, "1", root, true, true); + }, + 'only-of-type': function(nodes, formula, root) { + var p = Selector.pseudos; + return p['last-of-type'](p['first-of-type'](nodes, formula, root), formula, root); + }, + + // handles the an+b logic + getIndices: function(a, b, total) { + if (a == 0) return b > 0 ? [b] : []; + return $R(1, total).inject([], function(memo, i) { + if (0 == (i - b) % a && (i - b) / a >= 0) memo.push(i); + return memo; + }); + }, + + // handles nth(-last)-child, nth(-last)-of-type, and (first|last)-of-type + nth: function(nodes, formula, root, reverse, ofType) { + if (nodes.length == 0) return []; + if (formula == 'even') formula = '2n+0'; + if (formula == 'odd') formula = '2n+1'; + var h = Selector.handlers, results = [], indexed = [], m; + h.mark(nodes); + for (var i = 0, node; node = nodes[i]; i++) { + if (!node.parentNode._countedByPrototype) { + h.index(node.parentNode, reverse, ofType); + indexed.push(node.parentNode); + } + } + if (formula.match(/^\d+$/)) { // just a number + formula = Number(formula); + for (var i = 0, node; node = nodes[i]; i++) + if (node.nodeIndex == formula) results.push(node); + } else if (m = formula.match(/^(-?\d*)?n(([+-])(\d+))?/)) { // an+b + if (m[1] == "-") m[1] = -1; + var a = m[1] ? Number(m[1]) : 1; + var b = m[2] ? Number(m[2]) : 0; + var indices = Selector.pseudos.getIndices(a, b, nodes.length); + for (var i = 0, node, l = indices.length; node = nodes[i]; i++) { + for (var j = 0; j < l; j++) + if (node.nodeIndex == indices[j]) results.push(node); + } + } + h.unmark(nodes); + h.unmark(indexed); + return results; + }, + + 'empty': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) { + // IE treats comments as element nodes + if (node.tagName == '!' || node.firstChild) continue; + results.push(node); + } + return results; + }, + + 'not': function(nodes, selector, root) { + var h = Selector.handlers, selectorType, m; + var exclusions = new Selector(selector).findElements(root); + h.mark(exclusions); + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!node._countedByPrototype) results.push(node); + h.unmark(exclusions); + return results; + }, + + 'enabled': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (!node.disabled && (!node.type || node.type !== 'hidden')) + results.push(node); + return results; + }, + + 'disabled': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (node.disabled) results.push(node); + return results; + }, + + 'checked': function(nodes, value, root) { + for (var i = 0, results = [], node; node = nodes[i]; i++) + if (node.checked) results.push(node); + return results; + } + }, + + operators: { + '=': function(nv, v) { return nv == v; }, + '!=': function(nv, v) { return nv != v; }, + '^=': function(nv, v) { return nv == v || nv && nv.startsWith(v); }, + '$=': function(nv, v) { return nv == v || nv && nv.endsWith(v); }, + '*=': function(nv, v) { return nv == v || nv && nv.include(v); }, + '$=': function(nv, v) { return nv.endsWith(v); }, + '*=': function(nv, v) { return nv.include(v); }, + '~=': function(nv, v) { return (' ' + nv + ' ').include(' ' + v + ' '); }, + '|=': function(nv, v) { return ('-' + (nv || "").toUpperCase() + + '-').include('-' + (v || "").toUpperCase() + '-'); } + }, + + split: function(expression) { + var expressions = []; + expression.scan(/(([\w#:.~>+()\s-]+|\*|\[.*?\])+)\s*(,|$)/, function(m) { + expressions.push(m[1].strip()); + }); + return expressions; + }, + + matchElements: function(elements, expression) { + var matches = $$(expression), h = Selector.handlers; + h.mark(matches); + for (var i = 0, results = [], element; element = elements[i]; i++) + if (element._countedByPrototype) results.push(element); + h.unmark(matches); + return results; + }, + + findElement: function(elements, expression, index) { + if (Object.isNumber(expression)) { + index = expression; expression = false; + } + return Selector.matchElements(elements, expression || '*')[index || 0]; + }, + + findChildElements: function(element, expressions) { + expressions = Selector.split(expressions.join(',')); + var results = [], h = Selector.handlers; + for (var i = 0, l = expressions.length, selector; i < l; i++) { + selector = new Selector(expressions[i].strip()); + h.concat(results, selector.findElements(element)); + } + return (l > 1) ? h.unique(results) : results; + } +}); + +if (Prototype.Browser.IE) { + Object.extend(Selector.handlers, { + // IE returns comment nodes on getElementsByTagName("*"). + // Filter them out. + concat: function(a, b) { + for (var i = 0, node; node = b[i]; i++) + if (node.tagName !== "!") a.push(node); + return a; + }, + + // IE improperly serializes _countedByPrototype in (inner|outer)HTML. + unmark: function(nodes) { + for (var i = 0, node; node = nodes[i]; i++) + node.removeAttribute('_countedByPrototype'); + return nodes; + } + }); +} + +function $$() { + return Selector.findChildElements(document, $A(arguments)); +} +var Form = { + reset: function(form) { + $(form).reset(); + return form; + }, + + serializeElements: function(elements, options) { + if (typeof options != 'object') options = { hash: !!options }; + else if (Object.isUndefined(options.hash)) options.hash = true; + var key, value, submitted = false, submit = options.submit; + + var data = elements.inject({ }, function(result, element) { + if (!element.disabled && element.name) { + key = element.name; value = $(element).getValue(); + if (value != null && element.type != 'file' && (element.type != 'submit' || (!submitted && + submit !== false && (!submit || key == submit) && (submitted = true)))) { + if (key in result) { + // a key is already present; construct an array of values + if (!Object.isArray(result[key])) result[key] = [result[key]]; + result[key].push(value); + } + else result[key] = value; + } + } + return result; + }); + + return options.hash ? data : Object.toQueryString(data); + } +}; + +Form.Methods = { + serialize: function(form, options) { + return Form.serializeElements(Form.getElements(form), options); + }, + + getElements: function(form) { + return $A($(form).getElementsByTagName('*')).inject([], + function(elements, child) { + if (Form.Element.Serializers[child.tagName.toLowerCase()]) + elements.push(Element.extend(child)); + return elements; + } + ); + }, + + getInputs: function(form, typeName, name) { + form = $(form); + var inputs = form.getElementsByTagName('input'); + + if (!typeName && !name) return $A(inputs).map(Element.extend); + + for (var i = 0, matchingInputs = [], length = inputs.length; i < length; i++) { + var input = inputs[i]; + if ((typeName && input.type != typeName) || (name && input.name != name)) + continue; + matchingInputs.push(Element.extend(input)); + } + + return matchingInputs; + }, + + disable: function(form) { + form = $(form); + Form.getElements(form).invoke('disable'); + return form; + }, + + enable: function(form) { + form = $(form); + Form.getElements(form).invoke('enable'); + return form; + }, + + findFirstElement: function(form) { + var elements = $(form).getElements().findAll(function(element) { + return 'hidden' != element.type && !element.disabled; + }); + var firstByIndex = elements.findAll(function(element) { + return element.hasAttribute('tabIndex') && element.tabIndex >= 0; + }).sortBy(function(element) { return element.tabIndex }).first(); + + return firstByIndex ? firstByIndex : elements.find(function(element) { + return ['input', 'select', 'textarea'].include(element.tagName.toLowerCase()); + }); + }, + + focusFirstElement: function(form) { + form = $(form); + form.findFirstElement().activate(); + return form; + }, + + request: function(form, options) { + form = $(form), options = Object.clone(options || { }); + + var params = options.parameters, action = form.readAttribute('action') || ''; + if (action.blank()) action = window.location.href; + options.parameters = form.serialize(true); + + if (params) { + if (Object.isString(params)) params = params.toQueryParams(); + Object.extend(options.parameters, params); + } + + if (form.hasAttribute('method') && !options.method) + options.method = form.method; + + return new Ajax.Request(action, options); + } +}; + +/*--------------------------------------------------------------------------*/ + +Form.Element = { + focus: function(element) { + $(element).focus(); + return element; + }, + + select: function(element) { + $(element).select(); + return element; + } +}; + +Form.Element.Methods = { + serialize: function(element) { + element = $(element); + if (!element.disabled && element.name) { + var value = element.getValue(); + if (value != undefined) { + var pair = { }; + pair[element.name] = value; + return Object.toQueryString(pair); + } + } + return ''; + }, + + getValue: function(element) { + element = $(element); + var method = element.tagName.toLowerCase(); + return Form.Element.Serializers[method](element); + }, + + setValue: function(element, value) { + element = $(element); + var method = element.tagName.toLowerCase(); + Form.Element.Serializers[method](element, value); + return element; + }, + + clear: function(element) { + $(element).value = ''; + return element; + }, + + present: function(element) { + return $(element).value != ''; + }, + + activate: function(element) { + element = $(element); + try { + element.focus(); + if (element.select && (element.tagName.toLowerCase() != 'input' || + !['button', 'reset', 'submit'].include(element.type))) + element.select(); + } catch (e) { } + return element; + }, + + disable: function(element) { + element = $(element); + element.disabled = true; + return element; + }, + + enable: function(element) { + element = $(element); + element.disabled = false; + return element; + } +}; + +/*--------------------------------------------------------------------------*/ + +var Field = Form.Element; +var $F = Form.Element.Methods.getValue; + +/*--------------------------------------------------------------------------*/ + +Form.Element.Serializers = { + input: function(element, value) { + switch (element.type.toLowerCase()) { + case 'checkbox': + case 'radio': + return Form.Element.Serializers.inputSelector(element, value); + default: + return Form.Element.Serializers.textarea(element, value); + } + }, + + inputSelector: function(element, value) { + if (Object.isUndefined(value)) return element.checked ? element.value : null; + else element.checked = !!value; + }, + + textarea: function(element, value) { + if (Object.isUndefined(value)) return element.value; + else element.value = value; + }, + + select: function(element, value) { + if (Object.isUndefined(value)) + return this[element.type == 'select-one' ? + 'selectOne' : 'selectMany'](element); + else { + var opt, currentValue, single = !Object.isArray(value); + for (var i = 0, length = element.length; i < length; i++) { + opt = element.options[i]; + currentValue = this.optionValue(opt); + if (single) { + if (currentValue == value) { + opt.selected = true; + return; + } + } + else opt.selected = value.include(currentValue); + } + } + }, + + selectOne: function(element) { + var index = element.selectedIndex; + return index >= 0 ? this.optionValue(element.options[index]) : null; + }, + + selectMany: function(element) { + var values, length = element.length; + if (!length) return null; + + for (var i = 0, values = []; i < length; i++) { + var opt = element.options[i]; + if (opt.selected) values.push(this.optionValue(opt)); + } + return values; + }, + + optionValue: function(opt) { + // extend element because hasAttribute may not be native + return Element.extend(opt).hasAttribute('value') ? opt.value : opt.text; + } +}; + +/*--------------------------------------------------------------------------*/ + +Abstract.TimedObserver = Class.create(PeriodicalExecuter, { + initialize: function($super, element, frequency, callback) { + $super(callback, frequency); + this.element = $(element); + this.lastValue = this.getValue(); + }, + + execute: function() { + var value = this.getValue(); + if (Object.isString(this.lastValue) && Object.isString(value) ? + this.lastValue != value : String(this.lastValue) != String(value)) { + this.callback(this.element, value); + this.lastValue = value; + } + } +}); + +Form.Element.Observer = Class.create(Abstract.TimedObserver, { + getValue: function() { + return Form.Element.getValue(this.element); + } +}); + +Form.Observer = Class.create(Abstract.TimedObserver, { + getValue: function() { + return Form.serialize(this.element); + } +}); + +/*--------------------------------------------------------------------------*/ + +Abstract.EventObserver = Class.create({ + initialize: function(element, callback) { + this.element = $(element); + this.callback = callback; + + this.lastValue = this.getValue(); + if (this.element.tagName.toLowerCase() == 'form') + this.registerFormCallbacks(); + else + this.registerCallback(this.element); + }, + + onElementEvent: function() { + var value = this.getValue(); + if (this.lastValue != value) { + this.callback(this.element, value); + this.lastValue = value; + } + }, + + registerFormCallbacks: function() { + Form.getElements(this.element).each(this.registerCallback, this); + }, + + registerCallback: function(element) { + if (element.type) { + switch (element.type.toLowerCase()) { + case 'checkbox': + case 'radio': + Event.observe(element, 'click', this.onElementEvent.bind(this)); + break; + default: + Event.observe(element, 'change', this.onElementEvent.bind(this)); + break; + } + } + } +}); + +Form.Element.EventObserver = Class.create(Abstract.EventObserver, { + getValue: function() { + return Form.Element.getValue(this.element); + } +}); + +Form.EventObserver = Class.create(Abstract.EventObserver, { + getValue: function() { + return Form.serialize(this.element); + } +}); +if (!window.Event) var Event = { }; + +Object.extend(Event, { + KEY_BACKSPACE: 8, + KEY_TAB: 9, + KEY_RETURN: 13, + KEY_ESC: 27, + KEY_LEFT: 37, + KEY_UP: 38, + KEY_RIGHT: 39, + KEY_DOWN: 40, + KEY_DELETE: 46, + KEY_HOME: 36, + KEY_END: 35, + KEY_PAGEUP: 33, + KEY_PAGEDOWN: 34, + KEY_INSERT: 45, + + cache: { }, + + relatedTarget: function(event) { + var element; + switch(event.type) { + case 'mouseover': element = event.fromElement; break; + case 'mouseout': element = event.toElement; break; + default: return null; + } + return Element.extend(element); + } +}); + +Event.Methods = (function() { + var isButton; + + if (Prototype.Browser.IE) { + var buttonMap = { 0: 1, 1: 4, 2: 2 }; + isButton = function(event, code) { + return event.button == buttonMap[code]; + }; + + } else if (Prototype.Browser.WebKit) { + isButton = function(event, code) { + switch (code) { + case 0: return event.which == 1 && !event.metaKey; + case 1: return event.which == 1 && event.metaKey; + default: return false; + } + }; + + } else { + isButton = function(event, code) { + return event.which ? (event.which === code + 1) : (event.button === code); + }; + } + + return { + isLeftClick: function(event) { return isButton(event, 0) }, + isMiddleClick: function(event) { return isButton(event, 1) }, + isRightClick: function(event) { return isButton(event, 2) }, + + element: function(event) { + event = Event.extend(event); + + var node = event.target, + type = event.type, + currentTarget = event.currentTarget; + + if (currentTarget && currentTarget.tagName) { + // Firefox screws up the "click" event when moving between radio buttons + // via arrow keys. It also screws up the "load" and "error" events on images, + // reporting the document as the target instead of the original image. + if (type === 'load' || type === 'error' || + (type === 'click' && currentTarget.tagName.toLowerCase() === 'input' + && currentTarget.type === 'radio')) + node = currentTarget; + } + if (node.nodeType == Node.TEXT_NODE) node = node.parentNode; + return Element.extend(node); + }, + + findElement: function(event, expression) { + var element = Event.element(event); + if (!expression) return element; + var elements = [element].concat(element.ancestors()); + return Selector.findElement(elements, expression, 0); + }, + + pointer: function(event) { + var docElement = document.documentElement, + body = document.body || { scrollLeft: 0, scrollTop: 0 }; + return { + x: event.pageX || (event.clientX + + (docElement.scrollLeft || body.scrollLeft) - + (docElement.clientLeft || 0)), + y: event.pageY || (event.clientY + + (docElement.scrollTop || body.scrollTop) - + (docElement.clientTop || 0)) + }; + }, + + pointerX: function(event) { return Event.pointer(event).x }, + pointerY: function(event) { return Event.pointer(event).y }, + + stop: function(event) { + Event.extend(event); + event.preventDefault(); + event.stopPropagation(); + event.stopped = true; + } + }; +})(); + +Event.extend = (function() { + var methods = Object.keys(Event.Methods).inject({ }, function(m, name) { + m[name] = Event.Methods[name].methodize(); + return m; + }); + + if (Prototype.Browser.IE) { + Object.extend(methods, { + stopPropagation: function() { this.cancelBubble = true }, + preventDefault: function() { this.returnValue = false }, + inspect: function() { return "[object Event]" } + }); + + return function(event) { + if (!event) return false; + if (event._extendedByPrototype) return event; + + event._extendedByPrototype = Prototype.emptyFunction; + var pointer = Event.pointer(event); + Object.extend(event, { + target: event.srcElement, + relatedTarget: Event.relatedTarget(event), + pageX: pointer.x, + pageY: pointer.y + }); + return Object.extend(event, methods); + }; + + } else { + Event.prototype = Event.prototype || document.createEvent("HTMLEvents")['__proto__']; + Object.extend(Event.prototype, methods); + return Prototype.K; + } +})(); + +Object.extend(Event, (function() { + var cache = Event.cache; + + function getEventID(element) { + if (element._prototypeEventID) return element._prototypeEventID[0]; + arguments.callee.id = arguments.callee.id || 1; + return element._prototypeEventID = [++arguments.callee.id]; + } + + function getDOMEventName(eventName) { + if (eventName && eventName.include(':')) return "dataavailable"; + return eventName; + } + + function getCacheForID(id) { + return cache[id] = cache[id] || { }; + } + + function getWrappersForEventName(id, eventName) { + var c = getCacheForID(id); + return c[eventName] = c[eventName] || []; + } + + function createWrapper(element, eventName, handler) { + var id = getEventID(element); + var c = getWrappersForEventName(id, eventName); + if (c.pluck("handler").include(handler)) return false; + + var wrapper = function(event) { + if (!Event || !Event.extend || + (event.eventName && event.eventName != eventName)) + return false; + + Event.extend(event); + handler.call(element, event); + }; + + wrapper.handler = handler; + c.push(wrapper); + return wrapper; + } + + function findWrapper(id, eventName, handler) { + var c = getWrappersForEventName(id, eventName); + return c.find(function(wrapper) { return wrapper.handler == handler }); + } + + function destroyWrapper(id, eventName, handler) { + var c = getCacheForID(id); + if (!c[eventName]) return false; + c[eventName] = c[eventName].without(findWrapper(id, eventName, handler)); + } + + function destroyCache() { + for (var id in cache) + for (var eventName in cache[id]) + cache[id][eventName] = null; + } + + + // Internet Explorer needs to remove event handlers on page unload + // in order to avoid memory leaks. + if (window.attachEvent) { + window.attachEvent("onunload", destroyCache); + } + + // Safari has a dummy event handler on page unload so that it won't + // use its bfcache. Safari <= 3.1 has an issue with restoring the "document" + // object when page is returned to via the back button using its bfcache. + if (Prototype.Browser.WebKit) { + window.addEventListener('unload', Prototype.emptyFunction, false); + } + + return { + observe: function(element, eventName, handler) { + element = $(element); + var name = getDOMEventName(eventName); + + var wrapper = createWrapper(element, eventName, handler); + if (!wrapper) return element; + + if (element.addEventListener) { + element.addEventListener(name, wrapper, false); + } else { + element.attachEvent("on" + name, wrapper); + } + + return element; + }, + + stopObserving: function(element, eventName, handler) { + element = $(element); + var id = getEventID(element), name = getDOMEventName(eventName); + + if (!handler && eventName) { + getWrappersForEventName(id, eventName).each(function(wrapper) { + element.stopObserving(eventName, wrapper.handler); + }); + return element; + + } else if (!eventName) { + Object.keys(getCacheForID(id)).each(function(eventName) { + element.stopObserving(eventName); + }); + return element; + } + + var wrapper = findWrapper(id, eventName, handler); + if (!wrapper) return element; + + if (element.removeEventListener) { + element.removeEventListener(name, wrapper, false); + } else { + element.detachEvent("on" + name, wrapper); + } + + destroyWrapper(id, eventName, handler); + + return element; + }, + + fire: function(element, eventName, memo) { + element = $(element); + if (element == document && document.createEvent && !element.dispatchEvent) + element = document.documentElement; + + var event; + if (document.createEvent) { + event = document.createEvent("HTMLEvents"); + event.initEvent("dataavailable", true, true); + } else { + event = document.createEventObject(); + event.eventType = "ondataavailable"; + } + + event.eventName = eventName; + event.memo = memo || { }; + + if (document.createEvent) { + element.dispatchEvent(event); + } else { + element.fireEvent(event.eventType, event); + } + + return Event.extend(event); + } + }; +})()); + +Object.extend(Event, Event.Methods); + +Element.addMethods({ + fire: Event.fire, + observe: Event.observe, + stopObserving: Event.stopObserving +}); + +Object.extend(document, { + fire: Element.Methods.fire.methodize(), + observe: Element.Methods.observe.methodize(), + stopObserving: Element.Methods.stopObserving.methodize(), + loaded: false +}); + +(function() { + /* Support for the DOMContentLoaded event is based on work by Dan Webb, + Matthias Miller, Dean Edwards and John Resig. */ + + var timer; + + function fireContentLoadedEvent() { + if (document.loaded) return; + if (timer) window.clearInterval(timer); + document.fire("dom:loaded"); + document.loaded = true; + } + + if (document.addEventListener) { + if (Prototype.Browser.WebKit) { + timer = window.setInterval(function() { + if (/loaded|complete/.test(document.readyState)) + fireContentLoadedEvent(); + }, 0); + + Event.observe(window, "load", fireContentLoadedEvent); + + } else { + document.addEventListener("DOMContentLoaded", + fireContentLoadedEvent, false); + } + + } else { + document.write("